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= 007673
(593 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 243 bits (620), Expect = 2e-64, Method: Compositional matrix adjust.
Identities = 115/187 (61%), Positives = 146/187 (78%), Gaps = 2/187 (1%)
Query: 14 GPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
GP G + S + SLYVGDL +VT++ LY+ FS G +LS+RVCRD+ TRRSLGY
Sbjct: 1 GPLG-SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY 59
Query: 74 GYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKA 133
YVN+ PADA RALD +NF + K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KA
Sbjct: 60 AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKA 119
Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHF 193
L+DTFS+FGNILSCK+ D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F
Sbjct: 120 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178
Query: 194 LRKQERE 200
++ERE
Sbjct: 179 KSRKERE 185
Score = 105 bits (261), Expect = 9e-23, Method: Compositional matrix adjust.
Identities = 62/204 (30%), Positives = 110/204 (53%), Gaps = 6/204 (2%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 167
+PS ++++ +L + L++ FS G ILS ++ D + +S G+ +V F+
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 227
A+ A+D +N +I K V + +R+ K+ N+F+KNLD+S ++ L
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122
Query: 228 IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 287
F +G I S V+ D +G SK +GFV+FE + A +A+E +NG +DR+ +VG+ + +
Sbjct: 123 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
Query: 288 SEREQELKGQFEQAMKETVDKFQG 311
ERE EL + ++ V + G
Sbjct: 182 KEREAELGARAKEFYPYDVPDYAG 205
Score = 92.8 bits (229), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 70/200 (35%), Positives = 108/200 (54%), Gaps = 22/200 (11%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
+++V +L T+ L + F G I S V RD +S + +VNF+ DA +A++
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 269 LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
+N FD + GK + S+R+ L+ K V N++IKNL SID++
Sbjct: 77 MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 118
Query: 327 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 386
L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++ + ++V
Sbjct: 119 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 387 AQRKEERRARLQAQFSQMRP 406
+ ++ER A L A+ + P
Sbjct: 178 FKSRKEREAELGARAKEFYP 197
>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 = 243 bits (620), Expect = 2e-64, Method: Compositional matrix adjust.
Identities = 112/179 (62%), Positives = 142/179 (79%), Gaps = 1/179 (0%)
Query: 23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPA 82
S + SLYVGDL +VT++ LY+ FS G +LS+RVCRD+ TRRSLGY YVN+ PA
Sbjct: 4 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63
Query: 83 DAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG 142
DA RALD +NF + K +RIM+S RDPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FG
Sbjct: 64 DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 123
Query: 143 NILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
NILSCK+ D +G SKG+GFV FE +E+A+ AI+K+NGML+ND++VFVG F ++ERE
Sbjct: 124 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 181
Score = 103 bits (257), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 60/187 (32%), Positives = 104/187 (55%), Gaps = 6/187 (3%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 167
+PS ++++ +L + L++ FS G ILS ++ D + +S G+ +V F+
Sbjct: 2 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 61
Query: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 227
A+ A+D +N +I K V + +R+ K+ N+F+KNLD+S ++ L
Sbjct: 62 PADAERALDTMNFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 117
Query: 228 IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 287
F +G I S V+ D +G SK +GFV+FE + A +A+E +NG +DR+ +VG+ + +
Sbjct: 118 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 176
Query: 288 SEREQEL 294
ERE EL
Sbjct: 177 KEREAEL 183
Score = 90.9 bits (224), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 69/194 (35%), Positives = 106/194 (54%), Gaps = 22/194 (11%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
+++V +L T+ L + F G I S V RD +S + +VNF+ DA +A++
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 269 LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
+N FD + GK + S+R+ L+ K V N++IKNL SID++
Sbjct: 72 MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 113
Query: 327 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 386
L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++ + ++V
Sbjct: 114 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172
Query: 387 AQRKEERRARLQAQ 400
+ ++ER A L A+
Sbjct: 173 FKSRKEREAELGAR 186
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 139 bits (350), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 64/93 (68%), Positives = 81/93 (87%), Gaps = 1/93 (1%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENK 168
DPS+RKSG GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+ D +G SKG+GFV FE +
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 169 ESAQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
E+A+ AI+K+NGML+ND++VFVG F ++ERE
Sbjct: 62 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 94
Score = 76.6 bits (187), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 39/83 (46%), Positives = 56/83 (67%), Gaps = 1/83 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
N++IKNL SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
NG ++ + ++V + ++ER A
Sbjct: 72 NGMLLNDRKVFVGRFKSRKEREA 94
Score = 69.3 bits (168), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 57/89 (64%), Gaps = 1/89 (1%)
Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
K+ N+F+KNLD+S ++ L F +G I S V+ D +G SK +GFV+FE + A +
Sbjct: 8 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAER 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQE 293
A+E +NG +DR+ +VG+ + + ERE E
Sbjct: 67 AIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
++++ +LD ++ + LYD FS G +LS +V D + S GYG+V++ A RA++
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 70
Query: 91 LNFTPLNNKSI 101
+N LN++ +
Sbjct: 71 MNGMLLNDRKV 81
>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 (337), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 65/108 (60%), Positives = 86/108 (79%), Gaps = 3/108 (2%)
Query: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
G+GNIFIKNLDKSID+KAL+DTFS+FGNILSCK+ D +G SKG+GFV FE +E+A+ AI
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 176 DKLNGMLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTT 221
+K+NGML+ND++VFVG F ++ERE A +F NV++KN +T
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110
Score = 79.7 bits (195), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 42/97 (43%), Positives = 62/97 (63%), Gaps = 1/97 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
N++IKNL SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 373 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAM 409
NG ++ + ++V + ++ER A L A+ + V +
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYI 102
Score = 75.5 bits (184), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 66/111 (59%), Gaps = 11/111 (9%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
N+F+KNLD+S ++ L F +G I S V+ D +G SK +GFV+FE + A +A+E +
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 320
NG +DR+ +VG+ + + ERE EL + ++ N+YIKN G
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGARAKEFT----------NVYIKNFG 106
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 55/103 (53%), Gaps = 8/103 (7%)
Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
+ ++++ +LD ++ + LYD FS G +LS +V D + S GYG+V++ A RA+
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAI 62
Query: 89 DVLNFTPLNNKSIRI----MYSHRDPSI--RKSGTGNIFIKNL 125
+ +N LN++ + + R+ + R N++IKN
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNF 105
>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum
Aevestium Poly(A)-Binding Protein
Length = 85
Score = 126 bits (316), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 63/79 (79%), Positives = 70/79 (88%)
Query: 495 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 554
PI AL++ALAN+ PE QR +LGE+LYPLV+QLE D AAKVTGMLLEMDQTEVLHLLESP+
Sbjct: 6 PIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPD 65
Query: 555 ALKAKVAEAMEVLRSVAQQ 573
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 = 4e-27, Method: Compositional matrix adjust.
Identities = 55/90 (61%), Positives = 75/90 (83%), Gaps = 1/90 (1%)
Query: 306 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 365
+ ++Q +NLY+KNL D IDDE+L++ FS FGTITS KVM + G SKG GFV FS+PEEA
Sbjct: 10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEA 68
Query: 366 SRALAEMNGKMIVSKPLYVAVAQRKEERRA 395
++A+ EMNG+++ +KPLYVA+AQRKEER++
Sbjct: 69 TKAVTEMNGRIVATKPLYVALAQRKEERQS 98
Score = 80.5 bits (197), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/82 (50%), Positives = 56/82 (68%), Gaps = 1/82 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
N++VKNLD+ DE L+K F +GTITSA VM +G G+SK FGFV F + ++A KAV +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 270 NGKKFDDREWYVGKAQKKSERE 291
NG+ + YV AQ+K ER+
Sbjct: 76 NGRIVATKPLYVALAQRKEERQ 97
Score = 76.6 bits (187), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 36/83 (43%), Positives = 54/83 (65%), Gaps = 1/83 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
N+++KNLD ID + L FS FG I S K+ +G G+SKGFGFV F + E A A+ ++
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 179 NGMLINDKQVFVGHFLRKQERET 201
NG ++ K ++V RK+ER++
Sbjct: 76 NGRIVATKPLYVALAQRKEERQS 98
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 56/101 (55%), Gaps = 6/101 (5%)
Query: 19 AAGASGNQ---FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
++G+SG++ + +LYV +LD + D +L FS G + S +V + RS G+G+
Sbjct: 2 SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGF 59
Query: 76 VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
V +++P +A +A+ +N + K + + + R R+SG
Sbjct: 60 VCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE-RQSG 99
>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 = 107 bits (268), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 56/152 (36%), Positives = 90/152 (59%), Gaps = 3/152 (1%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L N+T + LF +G++ S ++ RD T +SLGYG+VNY +P DA +A++
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
LN L K+I++ Y+ PS N+++ L K++ K L FS +G I++ +I
Sbjct: 63 TLNGLRLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 150 ATDG-SGQSKGFGFVQFENKESAQNAIDKLNG 180
D +G S+G GF++F+ + A+ AI LNG
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 84.3 bits (207), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 49/157 (31%), Positives = 90/157 (57%), Gaps = 8/157 (5%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
N+ + L +++ + F S G I SCK+ D +GQS G+GFV + + + A+ AI+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG-TIT 236
LNG+ + K + V + R + A + N++V L ++ T ++L+++F +YG IT
Sbjct: 64 LNGLRLQTKTIKVSY-----ARPSSA-SIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 237 SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK 273
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: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 267
N+ V L ++ T E+ + +FG G I S ++RD G+S +GFVN+ + DA KA+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEK 327
LNG + + V A+ S + NLY+ L ++ ++
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMTQKE 104
Query: 328 LKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK 375
L++LFS++G I + +++ D +G+S+G GF+ F EA A+ +NG+
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
NL + L ++ E+ + LF G I SCK++RD +G S G GFV + P++A +A+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 372 MNGKMIVSKPLYVAVAQ 388
+NG + +K + V+ A+
Sbjct: 64 LNGLRLQTKTIKVSYAR 80
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 105 bits (262), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 55/152 (36%), Positives = 90/152 (59%), Gaps = 3/152 (1%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L N+T + LF +G + S ++ RD T +SLGYG+VNY++P DA +A++
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
LN L K+I++ Y+ PS N+++ L K++ K + FS +G I++ +I
Sbjct: 65 TLNGLKLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 180
D +G S+G GF++F+ + A+ AI LNG
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 54/178 (30%), Positives = 92/178 (51%), Gaps = 24/178 (13%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
N+ V L ++ T ++ K +FG G I S ++RD G+S +GFVN+ + +DA KA+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
LNG K + V A+ S + NLY+ L ++ +++
Sbjct: 66 LNGLKLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMSQKEM 107
Query: 329 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA 385
++LFS++G I + +++ D +G+S+G GF+ F EA A+ +NG+ KPL A
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ----KPLGAA 161
Score = 82.0 bits (201), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 46/157 (29%), Positives = 88/157 (56%), Gaps = 8/157 (5%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
N+ + L +++ F S G+I SCK+ D +GQS G+GFV + + A AI+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG-TIT 236
LNG+ + K + V + + +I+ N++V L ++ + ++++++F +YG IT
Sbjct: 66 LNGLKLQTKTIKVSY----ARPSSASIRDA--NLYVSGLPKTMSQKEMEQLFSQYGRIIT 119
Query: 237 SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK 273
S +++ G S+ GF+ F+ +A +A++ LNG+K
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 156
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: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
NL + L ++ ++ K LF G I SCK++RD +G S G GFV +S P +A +A+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 372 MNGKMIVSKPLYVAVAQ 388
+NG + +K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
>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 = 105 bits (262), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 56/152 (36%), Positives = 88/152 (57%), Gaps = 3/152 (1%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L N+T +L LFS +G+V S ++ RD SLGYG+VNY DA RA++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
LN L +K+I++ Y+ PS N++I L +++ K + D FS FG I++ ++
Sbjct: 63 TLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 180
D +G S+G F++F+ + A+ AI NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
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: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
LNG + + V A+ SE +K+ NLYI L ++ + +
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 329 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 374
+++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: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 174
G N+ + L +++ L FSS G + S K+ D +G S G+GFV + + A+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 175 IDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 234
I+ LNG+ + K + V + + E + K N+++ L + T +D++ +F +G
Sbjct: 61 INTLNGLRLQSKTIKVSY--ARPSSEVI----KDANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 235 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKK 273
I ++ V+ D G S+ F+ F+ +A +A+ + NG K
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 372 MNGKMIVSKPLYVAVAQRKEE 392
+NG + SK + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 105 bits (261), Expect = 9e-23, Method: Compositional matrix adjust.
Identities = 56/152 (36%), Positives = 88/152 (57%), Gaps = 3/152 (1%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L N+T +L LFS +G+V S ++ RD SLGYG+VNY DA RA++
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
LN L +K+I++ Y+ PS N++I L +++ K + D FS FG I++ ++
Sbjct: 63 TLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 150 ATD-GSGQSKGFGFVQFENKESAQNAIDKLNG 180
D +G S+G F++F+ + A+ AI NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 82.0 bits (201), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 56/186 (30%), Positives = 92/186 (49%), Gaps = 22/186 (11%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
LNG + + V A+ SE +K+ NLYI L ++ + +
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 329 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVA 385
+++FS FG I + +V+ D +G+S+G F+ F EA A+ NG S+P+ V
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVX 165
Query: 386 VAQRKE 391
A E
Sbjct: 166 FAANLE 171
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: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 174
G N+ + L +++ L FSS G + S K+ D +G S G+GFV + + A+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 175 IDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 234
I+ LNG+ + K + V + + E + K N+++ L + T +D++ +F +G
Sbjct: 61 INTLNGLRLQSKTIKVSY--ARPSSEVI----KDANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 235 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKK 273
I ++ V+ D G S+ F+ F+ +A +A+ + NG K
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 372 MNGKMIVSKPLYVAVAQRKEE 392
+NG + SK + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 92.0 bits (227), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 85/154 (55%), Gaps = 3/154 (1%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L ++TD +LY LF +G + + R+ RD T S GY +V++ + D+ RA+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
VLN + NK +++ Y+ P N+++ NL ++I L F +G+I+ I
Sbjct: 64 VLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 150 ATDG-SGQSKGFGFVQFENKESAQNAIDKLNGML 182
D +G+ +G FV++ +E AQ AI LN ++
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Score = 84.3 bits (207), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 48/154 (31%), Positives = 83/154 (53%), Gaps = 8/154 (5%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
N+ + L + + + L+ F + G I +C+I D +G S G+ FV F ++ +Q AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 178 LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS 237
LNG+ + +K++ V + E K N++V NL + TD+ L IFG+YG+I
Sbjct: 65 LNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 238 AVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
++RD G+ + FV + ++A +A+ ALN
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 79.0 bits (193), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 54/182 (29%), Positives = 93/182 (51%), Gaps = 22/182 (12%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
N+ V L + TD +L +F G I + +MRD G S + FV+F + D+ +A++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
LNG ++ V A+ E ++K+T NLY+ NL +I D++L
Sbjct: 65 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 106
Query: 329 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 385
+F ++G+I ++RD +G +G FV ++ EEA A++ +N + S+PL V
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166
Query: 386 VA 387
+A
Sbjct: 167 LA 168
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
NL + L + D +L LF G I +C++MRD +G S G FV F++ ++ RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 372 MNGKMIVSKPLYVAVAQ 388
+NG + +K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 20 AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA 79
A G T+LYV +L +TD QL +F + G ++ + RD T R G +V Y
Sbjct: 80 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 139
Query: 80 NPADAARALDVLN 92
+A A+ LN
Sbjct: 140 KREEAQEAISALN 152
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 92.0 bits (227), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 84/154 (54%), Gaps = 3/154 (1%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L + TD +LY LF +G + + R+ RD T S GY +V++ + D+ RA+
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
VLN + NK +++ Y+ P N+++ NL ++I L F +G+I+ I
Sbjct: 75 VLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 150 ATDG-SGQSKGFGFVQFENKESAQNAIDKLNGML 182
D +G+ +G FV++ +E AQ AI LN ++
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
Score = 82.8 bits (203), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 53/164 (32%), Positives = 87/164 (53%), Gaps = 11/164 (6%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 167
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: 168 KESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKK 227
+ +Q AI LNG+ + +K++ V + E K N++V NL + TD+ L
Sbjct: 66 EXDSQRAIKVLNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDT 119
Query: 228 IFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 270
IFG+YG+I ++RD G+ + FV + ++A +A+ ALN
Sbjct: 120 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 76.6 bits (187), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 53/183 (28%), Positives = 93/183 (50%), Gaps = 22/183 (12%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
N+ V L + TD +L +F G I + + RD G S + FV+F + D+ +A++
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
LNG ++ V A+ E ++K+T NLY+ NL +I D++L
Sbjct: 76 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 117
Query: 329 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 385
+F ++G+I ++RD +G +G FV ++ EEA A++ +N + S+PL V
Sbjct: 118 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 177
Query: 386 VAQ 388
+A+
Sbjct: 178 LAE 180
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 20 AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA 79
A G T+LYV +L +TD QL +F + G ++ + RD T R G +V Y
Sbjct: 91 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 150
Query: 80 NPADAARALDVLN 92
+A A+ LN
Sbjct: 151 KREEAQEAISALN 163
>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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
++V NLD++ T++ LK+ F G I + +M D + K+ + FV + + DA A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 271 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 330
GK+ ++ + A F+ + D F NL++ +L ++DDE L+
Sbjct: 63 GKQIENNIVKINWA-------------FQSQQSSSDDTF---NLFVGDLNVNVDDETLRN 106
Query: 331 LFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR 389
F +F + S VM D +G S+G GFV+F++ ++A A+ M G+ + +PL + A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 82.8 bits (203), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 47/154 (30%), Positives = 84/154 (54%), Gaps = 2/154 (1%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LYVG+LD +T+ L F G + ++++ D +++ Y +V Y DA AL L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIAT 151
N + N ++I ++ + T N+F+ +L+ ++D + L + F F + LS +
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 152 D-GSGQSKGFGFVQFENKESAQNAIDKLNGMLIN 184
D +G S+G+GFV F +++ AQNA+D + G +N
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 155
Score = 72.4 bits (176), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 85/168 (50%), Gaps = 5/168 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+++ NLDK+I L F G I + KI D + ++ + FV++ A A+ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 239
G I + V + + Q+ + F N+FV +L+ + DE L+ F ++ + S
Sbjct: 63 GKQIENNIVKINWAFQSQQSSS---DDTF-NLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Query: 240 VMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK 286
VM D G S+ +GFV+F + DDA A++++ G+ + R + A K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 45/80 (56%)
Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
T +L+VGDL+ NV D L + F LS V D+ T S GYG+V++ + DA A+
Sbjct: 87 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 146
Query: 89 DVLNFTPLNNKSIRIMYSHR 108
D + LN + +RI ++ +
Sbjct: 147 DSMQGQDLNGRPLRINWAAK 166
>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 = 82.8 bits (203), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 92/172 (53%), Gaps = 7/172 (4%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+++ ++ + + F+ FG I S ++ D + + KGF FV++E E+AQ A++++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKTK-----FNNVFVKNLDESTTDEDLKKIFGEYG 233
N +++ + + VG + + + + FN ++V ++ + +D+D+K +F +G
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 234 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
I SA + RD GK K +GF+ +E A + AV ++N + VGKA
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 255
Q + +AI ++ V+V ++ ++ +++ F +G I S + D K K F FV
Sbjct: 20 QRQGALAIMSR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 314
+E + A A+E +N R VG+ GQ + + + ++ + N +
Sbjct: 77 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 128
Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
Y+ ++ + D+ +K +F FG I S + RDP +G KG GF+ + + + A++ MN
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 37/72 (51%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+YV + +++D + +F G++ S + RD +T + GYG++ Y + A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 92 NFTPLNNKSIRI 103
N L + +R+
Sbjct: 188 NLFDLGGQYLRV 199
Score = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 12/94 (12%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS-KGSGFVAFSTPEEASRALAEM 372
+Y+ ++ + ++ +++ F+ FG I S + D + KG FV + PE A AL +M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 373 NGKMI------VSKPLYVAVAQR-----KEERRA 395
N M+ V +P + AQ EE RA
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124
>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
Binding Protein
Length = 144
Score = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 495 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 554
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 52 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 109
Query: 555 ALKAKVAEAMEVLRS 569
+L++KV EA+ VL++
Sbjct: 110 SLRSKVDEAVAVLQA 124
>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 = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 495 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 554
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 555 ALKAKVAEAMEVLRS 569
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>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: 499 LSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKA 558
LST LAN +PEQQ+ +LGE LY + + AAAKVTGMLLEMD E+L+LL++P L A
Sbjct: 11 LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDA 70
Query: 559 KVAEAMEVL 567
KV EA+EVL
Sbjct: 71 KVQEALEVL 79
>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 = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 495 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 554
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 555 ALKAKVAEAMEVLRS 569
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>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 = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 495 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 554
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 555 ALKAKVAEAMEVLRS 569
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 495 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 554
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 5 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 62
Query: 555 ALKAKVAEAMEVLRS 569
+L++KV EA+ VL++
Sbjct: 63 SLRSKVDEAVAVLQA 77
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
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: 495 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 554
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 4 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 61
Query: 555 ALKAKVAEAMEVLRS 569
+L++KV EA+ VL++
Sbjct: 62 SLRSKVDEAVAVLQA 76
>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 = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 45/172 (26%), Positives = 91/172 (52%), Gaps = 7/172 (4%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+++ ++ + + F+ FG I S ++ D + + KGF FV++E E+AQ A++++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLDESTTDEDLKKIFGEYG 233
N +++ + + VG + + + + FN ++V ++ + +D+D+K +F +G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 234 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
I S + RD GK K +GF+ +E A + AV ++N + VGKA
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 46/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 255
Q + +AI + V+V ++ ++ +++ F +G I S + D K K F FV
Sbjct: 5 QRQRALAIMCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 61
Query: 256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 314
+E + A A+E +N R VG+ GQ + + + ++ + N +
Sbjct: 62 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 113
Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
Y+ ++ + D+ +K +F FG I SC + RDP +G KG GF+ + + + A++ MN
Sbjct: 114 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 37/72 (51%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+YV + +++D + +F G++ S + RD +T + GYG++ Y + A+ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 92 NFTPLNNKSIRI 103
N L + +R+
Sbjct: 173 NLFDLGGQYLRV 184
Score = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS-KGSGFVAFSTPEEASRALAEM 372
+Y+ ++ + ++ +++ F+ FG I S + D + KG FV + PE A AL +M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 373 NGKMI------VSKPLYVAVAQ 388
N M+ V +P + AQ
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQ 97
>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 = 79.7 bits (195), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 37/76 (48%), Positives = 61/76 (80%), Gaps = 1/76 (1%)
Query: 495 PITALSTA-LANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESP 553
P+ +L+ + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESP
Sbjct: 2 PLGSLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 61
Query: 554 EALKAKVAEAMEVLRS 569
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 = 1e-13, Method: Compositional matrix adjust.
Identities = 45/172 (26%), Positives = 87/172 (50%), Gaps = 7/172 (4%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+++ ++ + + F+ FG I S + D + + KGF FV++E E+AQ A+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLDESTTDEDLKKIFGEYG 233
N + + + + VG + + + + FN ++V ++ + +D+D+K +F +G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 234 TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 284
I S + RD GK K +GF+ +E A + AV + N + VGKA
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 83/180 (46%), Gaps = 14/180 (7%)
Query: 197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 255
Q + +AI + V+V ++ ++ +++ F +G I S D K K F FV
Sbjct: 4 QRQRALAIXCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVE 60
Query: 256 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 314
+E + A A+E N R VG+ GQ + + + ++ + N +
Sbjct: 61 YEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 112
Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 373
Y+ ++ + D+ +K +F FG I SC + RDP +G KG GF+ + + + A++ N
Sbjct: 113 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 36/72 (50%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+YV + +++D + +F G++ S + RD +T + GYG++ Y + A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 92 NFTPLNNKSIRI 103
N L + +R+
Sbjct: 172 NLFDLGGQYLRV 183
>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 = 72.8 bits (177), Expect = 5e-13, Method: Composition-based stats.
Identities = 45/162 (27%), Positives = 87/162 (53%), Gaps = 28/162 (17%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFE---NADDAAKAV 266
+F+ L+ TT+++L++ FG+YGT+T +M+D G+S+ FGF++FE + D+ K
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 267 EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 326
L+GK D + +A + E+++ K +++ +G + +
Sbjct: 66 HILDGKVIDPK-----RAIPRDEQDKTGK------------------IFVGGIGPDVRPK 102
Query: 327 KLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 367
+ +E FS++GTI ++M D +G S+G GFV + + + R
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
Score = 66.6 bits (161), Expect = 4e-11, Method: Composition-based stats.
Identities = 36/143 (25%), Positives = 76/143 (53%), Gaps = 5/143 (3%)
Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
+ +++G L+++ T+ L + F + G V +++ +D +T RS G+G++++ P+ +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 89 DVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCK 148
+ L+ K I P + TG IF+ + + K + FS +G I+ +
Sbjct: 63 KTQHI--LDGKVIDP--KRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 149 IATD-GSGQSKGFGFVQFENKES 170
+ D +GQS+GFGFV +++ ++
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADA 141
Score = 65.5 bits (158), Expect = 9e-11, Method: Composition-based stats.
Identities = 49/176 (27%), Positives = 88/176 (50%), Gaps = 23/176 (13%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK- 177
+FI L+ L + F +G + KI D +G+S+GFGF+ FE S +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 178 --LNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTI 235
L+G +I+ K+ + + E++ K +FV + ++ ++ F ++GTI
Sbjct: 66 HILDGKVIDPKRA-----IPRDEQD------KTGKIFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 236 TSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKK---FDDREWYVGKAQKK 287
A +M D D G+S+ FGFV +++AD AV+ + K F DR+ + +A+ +
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSAD----AVDRVCQNKFIDFKDRKIEIKRAEPR 166
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP---EEA 365
+ ++I L ++ L+E F ++GT+T K+M+DP +G S+G GF++F P +E
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 366 SRALAEMNGKMIVSK 380
+ ++GK+I K
Sbjct: 62 VKTQHILDGKVIDPK 76
Score = 35.8 bits (81), Expect = 0.073, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
T ++VG + +V + + FSQ G ++ ++ D T +S G+G+V Y + ADA +
Sbjct: 87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSADAVDRV 145
Query: 89 DVLNFTPLNNKSIRI 103
F ++ I I
Sbjct: 146 CQNKFIDFKDRKIEI 160
>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 = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 57/178 (32%), Positives = 81/178 (45%), Gaps = 19/178 (10%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN--PADAARALD 89
L++G L F TD L F Q G + V RD +T+RS G+G+V YA DAA
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 71
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFG 142
+N P + R++ R S S IF+ + + + L D F +G
Sbjct: 72 -MNARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 143 NILSCKIATD-GSGQSKGFGFVQFENKESAQN-AIDKLNGMLINDKQVFVGHFLRKQE 198
I +I TD GSG+ +GF FV F++ +S I K + +N V L KQE
Sbjct: 130 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 185
Score = 59.3 bits (142), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 72 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
L++ F ++G I ++M D SG +G FV F
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPAD 83
G ++VG + + + L D F Q G++ + + D + + G+ +V + + D
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHD 157
Query: 84 AARALDVLNFTPLNNKSIRI 103
+ + + + +N + +
Sbjct: 158 SVDKIVIQKYHTVNGHNCEV 177
>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 = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 57/178 (32%), Positives = 81/178 (45%), Gaps = 19/178 (10%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN--PADAARALD 89
L++G L F TD L F Q G + V RD +T+RS G+G+V YA DAA
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 70
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFG 142
+N P + R++ R S S IF+ + + + L D F +G
Sbjct: 71 -MNARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 128
Query: 143 NILSCKIATD-GSGQSKGFGFVQFENKESAQN-AIDKLNGMLINDKQVFVGHFLRKQE 198
I +I TD GSG+ +GF FV F++ +S I K + +N V L KQE
Sbjct: 129 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 184
Score = 58.9 bits (141), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 71 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 117
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
L++ F ++G I ++M D SG +G FV F
Sbjct: 118 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPAD 83
G ++VG + + + L D F Q G++ + + D + + G+ +V + + D
Sbjct: 98 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHD 156
Query: 84 AARALDVLNFTPLNNKSIRI 103
+ + + + +N + +
Sbjct: 157 SVDKIVIQKYHTVNGHNCEV 176
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 57/178 (32%), Positives = 81/178 (45%), Gaps = 19/178 (10%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN--PADAARALD 89
L++G L F TD L F Q G + V RD +T+RS G+G+V YA DAA
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 72
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFG 142
+N P + R++ R S S IF+ + + + L D F +G
Sbjct: 73 -MNARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 130
Query: 143 NILSCKIATD-GSGQSKGFGFVQFENKESAQN-AIDKLNGMLINDKQVFVGHFLRKQE 198
I +I TD GSG+ +GF FV F++ +S I K + +N V L KQE
Sbjct: 131 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 186
Score = 58.9 bits (141), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 73 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 119
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
L++ F ++G I ++M D SG +G FV F
Sbjct: 120 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPAD 83
G ++VG + + + L D F Q G++ + + D + + G+ +V + + D
Sbjct: 100 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHD 158
Query: 84 AARALDVLNFTPLNNKSIRI 103
+ + + + +N + +
Sbjct: 159 SVDKIVIQKYHTVNGHNCEV 178
>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 = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 36/83 (43%), Positives = 58/83 (69%)
Query: 497 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEAL 556
T ++ LA+A P++Q+ LGE L+PL++ A K+TG LLE+D +E+L+ LESPE+L
Sbjct: 6 TLTASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLESPESL 65
Query: 557 KAKVAEAMEVLRSVAQQQANNPA 579
++KV EA+ VL++ ++A A
Sbjct: 66 RSKVDEAVAVLQAHQAKEATQKA 88
>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 = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 49/154 (31%), Positives = 72/154 (46%), Gaps = 16/154 (10%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN--PADAARALD 89
L++G L F TD L F Q G + V RD +T+RS G+G+V YA DAA
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 64
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFG 142
+N P + R++ R S S IF+ + + + L D F +G
Sbjct: 65 -MNARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 122
Query: 143 NILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
I +I TD GSG+ +GF FV F++ +S +
Sbjct: 123 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 58.9 bits (141), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 65 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 111
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
L++ F ++G I ++M D SG +G FV F
Sbjct: 112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 24 GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPAD 83
G ++VG + + + L D F Q G++ + + D + + G+ +V + + D
Sbjct: 92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHD 150
Query: 84 AARALDVLNFTPLNNKSIRI 103
+ + + + +N + +
Sbjct: 151 SVDKIVIQKYHTVNGHNCEV 170
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 67.0 bits (162), Expect = 3e-11, Method: Composition-based stats.
Identities = 47/152 (30%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L++G L F TD L F Q G + V RD +T+RS G+G+V YA + A +
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 70
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
N P + R++ R S S IF+ + + + L D F +G I
Sbjct: 71 NARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 129
Query: 145 LSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
+I TD GSG+ +GF FV F++ +S +
Sbjct: 130 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
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: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 176
+FI L ++L F +G + C + D + +S+GFGFV + E A++
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 177 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 234
K++G ++ K+ + +++ + +FV + E T + L+ F +YG
Sbjct: 74 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 128
Query: 235 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 266
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: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 70 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 116
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
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 = 67.0 bits (162), Expect = 3e-11, Method: Composition-based stats.
Identities = 47/152 (30%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L++G L F TD L F Q G + V RD +T+RS G+G+V YA + A +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKS-------GTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
N P + R++ R S S IF+ + + + L D F +G I
Sbjct: 73 NARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 145 LSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
+I TD GSG+ +GF FV F++ +S +
Sbjct: 132 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 61.2 bits (147), Expect = 2e-09, Method: Composition-based stats.
Identities = 40/153 (26%), Positives = 71/153 (46%), Gaps = 11/153 (7%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAID-- 176
+FI L ++L F +G + C + D + +S+GFGFV + E A++
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 177 --KLNGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT 234
K++G ++ K+ + +++ + +FV + E T + L+ F +YG
Sbjct: 76 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 235 ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 266
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: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 265
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 72 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 326 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 359
L++ F ++G I ++M D SG +G FV F
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 66.2 bits (160), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 83/188 (44%), Gaps = 30/188 (15%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVE 267
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 322
AL+ K L G Q + A E + + L+I +
Sbjct: 78 ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 118
Query: 323 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV---S 379
+ ++ +FS FG I C+++R P G+S+G FV F+T A A+ M+ + S
Sbjct: 119 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 178
Query: 380 KPLYVAVA 387
P+ V A
Sbjct: 179 SPMVVKFA 186
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 44/156 (28%), Positives = 66/156 (42%), Gaps = 12/156 (7%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR--RSLGYGYVNYANPADAARALD 89
++VG + ++ L +LF Q G V + V RD S +S G +V + A A +
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGN------IFIKNLDKSIDHKALHDTFSSFGN 143
L+ N K + M+ S N +FI + K + FSSFG
Sbjct: 78 ALH----NMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 133
Query: 144 ILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
I C+I G S+G FV F + AQ AI ++
Sbjct: 134 IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS---GISKGSGFVAFSTPE---E 364
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 15 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 74
Query: 365 ASRALAEM 372
A AL M
Sbjct: 75 AQNALHNM 82
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 75/150 (50%), Gaps = 14/150 (9%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
+ L+VG+L ++T+ ++ LF + G+ V + +D G+G++ A A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 76
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKI 149
L+ PL K +R+ ++ + ++ ++NL + + ++ L + FS FG + +
Sbjct: 77 ELDNMPLRGKQLRVRFA--------CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVV 128
Query: 150 ATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
D G+ G G V+F K +A+ A+D+ +
Sbjct: 129 IVDDRGRPSGKGIVEFSGKPAARKALDRCS 158
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/156 (25%), Positives = 68/156 (43%), Gaps = 17/156 (10%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
+F+ NL I + + F +G I D KGFGF++ E + A+ A +L
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 78
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 238
+ M + KQ+ V ++ V+NL + ++E L++ F +G + A
Sbjct: 79 DNMPLRGKQL------------RVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERA 126
Query: 239 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF 274
VV+ D G+ G V F A KA++ + F
Sbjct: 127 VVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSF 162
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 70/164 (42%), Gaps = 29/164 (17%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
T+ + +FV NL T+E+++K+F +YG + +D K FGF+ E A A
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIA 74
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
L+ R ++L+ +F +L ++NL + +
Sbjct: 75 KVELDNMPL---------------RGKQLRVRF---------ACHSASLTVRNLPQYVSN 110
Query: 326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
E L+E FS FG + V+ D G G G V FS A +AL
Sbjct: 111 ELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
Q L++ NL I +E++++LF ++G + +D KG GF+ T A A
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAK 75
Query: 370 AEMNGKMIVSKPLYVAVA 387
E++ + K L V A
Sbjct: 76 VELDNMPLRGKQLRVRFA 93
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 83/188 (44%), Gaps = 30/188 (15%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVE 267
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 268 ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 322
AL+ K L G Q + A E + + L+I +
Sbjct: 66 ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 106
Query: 323 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV---S 379
+ ++ +FS FG I C+++R P G+S+G FV F+T A A+ M+ + S
Sbjct: 107 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 166
Query: 380 KPLYVAVA 387
P+ V A
Sbjct: 167 SPMVVKFA 174
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 44/156 (28%), Positives = 66/156 (42%), Gaps = 12/156 (7%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR--RSLGYGYVNYANPADAARALD 89
++VG + ++ L +LF Q G V + V RD S +S G +V + A A +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGN------IFIKNLDKSIDHKALHDTFSSFGN 143
L+ N K + M+ S N +FI + K + FSSFG
Sbjct: 66 ALH----NMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121
Query: 144 ILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
I C+I G S+G FV F + AQ AI ++
Sbjct: 122 IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS---GISKGSGFVAFSTPE---E 364
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 365 ASRALAEM 372
A AL M
Sbjct: 63 AQNALHNM 70
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 65.9 bits (159), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 35/87 (40%), Positives = 55/87 (63%), Gaps = 2/87 (2%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNIL-SCKIATD-GSGQSKGFGFVQFENKESAQ 172
SG+ IFI NLD ID K L+DTFS+FG IL + KI D +G SKG+ F+ F + +++
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQER 199
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 = 53/82 (64%), Gaps = 2/82 (2%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTIT-SCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
++I NL ID++ L + FS FG I + K+MRDP +G SKG F+ F++ + + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
MNG+ + ++P+ V+ A +K+ +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 52/89 (58%), Gaps = 5/89 (5%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVL-SVRVCRDLSTRRSLGYGYVNYA 79
G+SG ++ +++G+LD + + LYD FS G +L + ++ RD T S GY ++N+A
Sbjct: 1 GSSG----SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFA 56
Query: 80 NPADAARALDVLNFTPLNNKSIRIMYSHR 108
+ + A++ +N L N+ I + Y+ +
Sbjct: 57 SFDASDAAIEAMNGQYLCNRPITVSYAFK 85
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTIT-SAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 268
+F+ NLD ++ L F +G I + +MRD D G SK + F+NF + D + A+EA
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 269 LNGKKFDDREWYVGKAQKKSER 290
+NG+ +R V A KK +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
>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 = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/77 (42%), Positives = 48/77 (62%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L N+T +L LFS +G+V S ++ RD SLGYG+VNY DA RA++
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 90 VLNFTPLNNKSIRIMYS 106
LN L +K+I++ Y+
Sbjct: 65 TLNGLRLQSKTIKVSYA 81
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 372 MNGKMIVSKPLYVAVAQ 388
+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: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 269 LNGKKFDDREWYVGKAQ 285
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: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 174
G N+ + L +++ L FSS G + S K+ D +G S G+GFV + + A+ A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 175 IDKLNGMLINDKQVFVGH 192
I+ LNG+ + K + V +
Sbjct: 63 INTLNGLRLQSKTIKVSY 80
>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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 269
+FV L T ++ L+++F +YG I+ VV++D + +S+ FGFV FEN DDA A+ A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 270 NGKKFDDREWYVGKAQKKSE 289
NGK D R+ V +A K S+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSD 94
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 43/72 (59%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+VG L F+ + L +FS+ GQ+ V V +D T+RS G+G+V + N DA A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 92 NFTPLNNKSIRI 103
N ++ + IR+
Sbjct: 75 NGKSVDGRQIRV 86
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: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQ-SKGFGFVQFENKESAQN 173
S G +F+ L + ++L FS +G I + D Q S+GFGFV FEN + A++
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 174 AIDKLNGMLINDKQVFV 190
A+ +NG ++ +Q+ V
Sbjct: 70 AMMAMNGKSVDGRQIRV 86
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
L++ L +++ L+++FS++G I+ V++D + S+G GFV F ++A A+ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 373 NGKMIVSKPLYVAVAQRKEERRA 395
NGK + + + V A + + R+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRS 97
>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 = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 34/80 (42%), Positives = 48/80 (60%)
Query: 27 FLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
F T+L V L N T +L LFS +G+V S ++ RD SLGYG+VNY DA R
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 87 ALDVLNFTPLNNKSIRIMYS 106
A++ LN L +K+I++ Y+
Sbjct: 77 AINTLNGLRLQSKTIKVSYA 96
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 309 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 367
FQG NL + L + ++L+ LFS G + S K++RD +G S G GFV + T ++A R
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 368 ALAEMNGKMIVSKPLYVAVAQ 388
A+ +NG + SK + V+ A+
Sbjct: 77 AINTLNGLRLQSKTIKVSYAR 97
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 269 LNGKKFDDREWYVGKAQ 285
LNG + + V A+
Sbjct: 81 LNGLRLQSKTIKVSYAR 97
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
N+ + L ++ L FSS G + S K+ D +G S G+GFV + + A+ AI+
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 178 LNGMLINDKQVFVGH 192
LNG+ + K + V +
Sbjct: 81 LNGLRLQSKTIKVSY 95
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 49/78 (62%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L N+T + LF +G + S ++ RD T +SLGYG+VNY++P DA +A++
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 90 VLNFTPLNNKSIRIMYSH 107
LN L K+I++ Y+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
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: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
NL + L ++ ++ K LF G I SCK++RD +G S G GFV +S P +A +A+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 372 MNGKMIVSKPLYVAVAQ 388
+NG + +K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
N+ V L ++ T ++ K +FG G I S ++RD G+S +GFVN+ + +DA KA+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 269 LNGKKFDDREWYVGKAQKKS 288
LNG K + V A+ S
Sbjct: 66 LNGLKLQTKTIKVSYARPSS 85
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
N+ + L +++ F S G+I SCK+ D +GQS G+GFV + + A AI+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 178 LNGMLINDKQVFVGH 192
LNG+ + K + V +
Sbjct: 66 LNGLKLQTKTIKVSY 80
>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: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
T+ +FV NL T+ED K++F YG + + RD + FGF+ E+ A A
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIA 74
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 325
L+G R + A G L +KNL + +
Sbjct: 75 KAELDGTILKSRPLRIRFAT------------------------HGAALTVKNLSPVVSN 110
Query: 326 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
E L++ FS+FG + V+ D G + G GFV F+ A +AL
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154
Score = 62.8 bits (151), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 71/146 (48%), Gaps = 14/146 (9%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+VG+L ++T+ LF + G+ V + RD G+G++ + A A L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIAT 151
+ T L ++ +RI ++ + + +KNL + ++ L FS FG + +
Sbjct: 79 DGTILKSRPLRIRFA--------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130
Query: 152 DGSGQSKGFGFVQFENKESAQNAIDK 177
D G++ G GFV+F K A+ A+++
Sbjct: 131 DDRGRATGKGFVEFAAKPPARKALER 156
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 39/149 (26%), Positives = 68/149 (45%), Gaps = 17/149 (11%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
+F+ NL I + F +G I D +GFGF++ E++ A+ A +L
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 179 NGMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 238
+G ++ + + + T + VKNL ++E L++ F ++G + A
Sbjct: 79 DGTILKSRPL------------RIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKA 126
Query: 239 VVMRDGDGKSKCFGFVNFENADDAAKAVE 267
VV+ D G++ GFV F A KA+E
Sbjct: 127 VVVVDDRGRATGKGFVEFAAKPPARKALE 155
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: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
Q L++ NL I +E K LF +G + + RD +G GF+ + A A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAK 75
Query: 370 AEMNGKMIVSKPLYVAVA 387
AE++G ++ S+PL + A
Sbjct: 76 AELDGTILKSRPLRIRFA 93
>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 = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 73/166 (43%), Gaps = 27/166 (16%)
Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVEA 268
FV + + +++DL+++F +YG + V+RD +SK FV F A +A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 269 LNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDSI 323
L+ K L G Q + A E + + L+I +
Sbjct: 67 LHNXKV-------------------LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKC 107
Query: 324 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+ ++ FS FG I C+++R P G+S+G FV F+T A A+
Sbjct: 108 TENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 41/154 (26%), Positives = 62/154 (40%), Gaps = 18/154 (11%)
Query: 33 YVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTR--RSLGYGYVNYANPADAARALDV 90
+VG + ++ L +LF Q G V + V RD S +S G +V + A A +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 91 LNFTPLNNKSIRIMYSHRDPSIRKSGTG---------NIFIKNLDKSIDHKALHDTFSSF 141
L+ + +++ P K +FI + K + FSSF
Sbjct: 67 LH-------NXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSF 119
Query: 142 GNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
G I C+I G S+G FV F + AQ AI
Sbjct: 120 GQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 47/78 (60%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+F+ L+ T ++ LK +FG++G I+ ++++D KS+ F F+ FEN DA A + +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 271 GKKFDDREWYVGKAQKKS 288
GK + V +A+K S
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
G +FI L++ + K L F G I + D + +S+GF F+ FEN A+NA
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 178 LNGMLINDKQVFV 190
+NG ++ K + V
Sbjct: 68 MNGKSLHGKAIKV 80
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L+I L +++ LK +F + G I+ +++D + S+G F+ F P +A A +MN
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 374 GKMIVSKPLYVAVAQR 389
GK + K + V A++
Sbjct: 70 GKSLHGKAIKVEQAKK 85
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L++G L+ + L +F + G + V + +D T +S G+ ++ + NPADA A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSG 116
N L+ K+I++ + + PS + G
Sbjct: 69 NGKSLHGKAIKVEQA-KKPSFQSGG 92
>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 = 59.3 bits (142), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 56/100 (56%), Gaps = 3/100 (3%)
Query: 19 AAGASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
++G+SG + T++ ++VGDL +T + F+ G++ RV +D++T +S GYG+
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61
Query: 76 VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKS 115
V++ N DA A+ + L + IR ++ R P KS
Sbjct: 62 VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKS 101
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
++F+ +L I + + F+ FG I ++ D +G+SKG+GFV F NK A+NAI +
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 178 LNGMLINDKQVFVGHFLRK 196
+ G + +Q+ RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
+VFV +L T ED+K F +G I+ A V++D GKSK +GFV+F N DA A++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 269 LNGKKFDDRE 278
+ G+ R+
Sbjct: 77 MGGQWLGGRQ 86
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 50/89 (56%), Gaps = 4/89 (4%)
Query: 303 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 361
K+T + F ++++ +L I E +K F+ FG I+ +V++D +G SKG GFV+F
Sbjct: 10 KDTSNHF---HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 362 PEEASRALAEMNGKMIVSKPLYVAVAQRK 390
+A A+ +M G+ + + + A RK
Sbjct: 67 KWDAENAIQQMGGQWLGGRQIRTNWATRK 95
>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: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
NLYI NL S+D+++L+ + FG + S +++RD SG S+G GF + E+ +
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 373 NGKMIVSKP 381
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: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
N++I NL S+D + L + FG ++S +I D SG S+G GF + E+ E + I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 179 NGMLI 183
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: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
N+++ NL S +++L+ + +G + S ++RD G S+ GF E+ + +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 269 LNGK 272
NGK
Sbjct: 86 FNGK 89
Score = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLS-TRRSLGYGYVNYANPADA 84
T+LY+ +L ++ + +L ++ GQV+S R+ RD S T R +G+ + +A
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 81
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 58.9 bits (141), Expect = 8e-09, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 47/77 (61%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T+L V L ++TD +LY LF +G + + R+ RD T S GY +V++ + D+ RA+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 90 VLNFTPLNNKSIRIMYS 106
VLN + NK +++ Y+
Sbjct: 64 VLNGITVRNKRLKVSYA 80
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
NL + L + D +L LF G I +C++MRD +G S G FV F++ ++ RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 372 MNGKMIVSKPLYVAVAQ 388
+NG + +K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
Score = 42.0 bits (97), Expect = 8e-04, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
N+ V L + TD +L +F G I + +MRD G S + FV+F + D+ +A++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 269 LNGKKFDDREWYVGKAQKKSE 289
LNG ++ V A+ E
Sbjct: 65 LNGITVRNKRLKVSYARPGGE 85
>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: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 370
NL++ +L ++DDE L+ F +F + S VM D +G S+G GFV+F++ ++A A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 371 EMNGKMIVSKPLYVAVAQRKEE 392
M G+ + +PL + A + E
Sbjct: 62 SMQGQDLNGRPLRINWAAKLEH 83
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 44/78 (56%)
Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
T +L+VGDL+ NV D L + F LS V D+ T S GYG+V++ + DA A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 89 DVLNFTPLNNKSIRIMYS 106
D + LN + +RI ++
Sbjct: 61 DSMQGQDLNGRPLRINWA 78
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
T N+F+ +L+ ++D + L + F F + LS + D +G S+G+GFV F +++ AQNA+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 176 DKLNGMLINDK 186
D + G +N +
Sbjct: 61 DSMQGQDLNGR 71
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
N+FV +L+ + DE L+ F ++ + S VM D G S+ +GFV+F + DDA A+++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 269 LNGKKFDDREWYVGKAQK 286
+ G+ + R + A K
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 268
N+F+ +L + TD DL F +G + SA V D SKCFGFV+F+N D A A++A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 269 LNG 271
+NG
Sbjct: 102 MNG 104
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
N+FI +L + L TF FGN++S K+ D + SK FGFV F+N +SAQ AI
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 178 LNGMLINDKQV 188
+NG + K++
Sbjct: 102 MNGFQVGTKRL 112
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
+G NL+I +L D L F FG + S KV D + +SK GFV+F P+ A A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 369 LAEMNGKMIVSKPLYV 384
+ MNG + +K L V
Sbjct: 99 IKAMNGFQVGTKRLKV 114
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 12/93 (12%)
Query: 11 QMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRS 70
Q+ GP G +L++ L TD+ L F G V+S +V D T S
Sbjct: 34 QIEGPEGC------------NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLS 81
Query: 71 LGYGYVNYANPADAARALDVLNFTPLNNKSIRI 103
+G+V++ NP A A+ +N + K +++
Sbjct: 82 KCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV 114
>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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 51/90 (56%)
Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
+ +LYVG+L F T+ Q+Y+LFS+ G + + + D + + G+ +V Y + ADA A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 89 DVLNFTPLNNKSIRIMYSHRDPSIRKSGTG 118
+N T L+++ IR + R+ G G
Sbjct: 99 RYINGTRLDDRIIRTDWDAGFKEGRQYGRG 128
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 48/96 (50%), Gaps = 6/96 (6%)
Query: 192 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC- 250
HF E + +K K ++V NL TT+E + ++F + G I ++ D K+ C
Sbjct: 24 HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 251 FGFVNFENADDAAKAVEALNGKKFDDR----EWYVG 282
F FV + + DA A+ +NG + DDR +W G
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 118
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 54/106 (50%), Gaps = 3/106 (2%)
Query: 84 AARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGN 143
A R+ + + ++ R ++ ++KS T +++ NL + +++ FS G+
Sbjct: 8 ALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCT--LYVGNLSFYTTEEQIYELFSKSGD 65
Query: 144 ILSCKIATDGSGQSK-GFGFVQFENKESAQNAIDKLNGMLINDKQV 188
I + D ++ GF FV++ ++ A+NA+ +NG ++D+ +
Sbjct: 66 IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII 111
Score = 28.9 bits (63), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 290 REQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-S 348
R+Q +G E+ +E + K + LY+ NL +E++ ELFS+ G I + D
Sbjct: 21 RDQHFRGDNEE--QEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK 77
Query: 349 GISKGSGFVAFSTPEEASRALAEMNG 374
+ G FV + + +A A+ +NG
Sbjct: 78 KTACGFCFVEYYSRADAENAMRYING 103
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 44/72 (61%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LYVG L FN+T+ L +F G++ S+++ D T RS GYG++ +++ A +AL+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 92 NFTPLNNKSIRI 103
N L + +++
Sbjct: 89 NGFELAGRPMKV 100
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: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
+ LY+ +L +I ++ L+ +F FG I S ++M D +G SKG GF+ FS E A +AL
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 371 EMNGKMIVSKPLYVA-VAQRKE 391
++NG + +P+ V V +R +
Sbjct: 87 QLNGFELAGRPMKVGHVTERTD 108
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQN 173
+G +++ +L +I L F FG I S ++ D +G+SKG+GF+ F + E A+
Sbjct: 24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83
Query: 174 AIDKLNGMLINDKQVFVGH 192
A+++LNG + + + VGH
Sbjct: 84 ALEQLNGFELAGRPMKVGH 102
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
++V +L + T++ L+ IF +G I S +M D + G+SK +GF+ F +++ A KA+E L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 270 NGKKFDDREWYVGKAQKKSE 289
NG + R VG ++++
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
>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 = 9e-08, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 48/80 (60%), Gaps = 4/80 (5%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKV--MRDPSGI--SKGSGFVAFSTPEEASRAL 369
L+IKNL S +E LK +FS+ G I SC + ++ +G+ S G GFV + PE+A +AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 370 AEMNGKMIVSKPLYVAVAQR 389
++ G + L V +++R
Sbjct: 68 KQLQGHTVDGHKLEVRISER 87
Score = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 34/91 (37%), Positives = 48/91 (52%), Gaps = 8/91 (8%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD----GSGQSKGFGFVQFENKES 170
SG+ +FIKNL+ S + L FS G I SC I+ G S GFGFV+++ E
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 171 AQNAIDKLNGMLINDKQVFVGHFLRKQERET 201
AQ A+ +L G ++ ++ V R ER T
Sbjct: 63 AQKALKQLQGHTVDGHKLEV----RISERAT 89
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK----SKCFGFVNFENADDAAK 264
+ +F+KNL+ STT+E LK +F + G I S + + + S FGFV ++ + A K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 265 AVEALNGKKFDDREWYV 281
A++ L G D + V
Sbjct: 66 ALKQLQGHTVDGHKLEV 82
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 47/91 (51%), Gaps = 7/91 (7%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRD---LSTRRSLGYGYVN 77
G+SG ++ L++ +L+F+ T+ L +FS+VG + S + + S+G+G+V
Sbjct: 1 GSSG----SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVE 56
Query: 78 YANPADAARALDVLNFTPLNNKSIRIMYSHR 108
Y P A +AL L ++ + + S R
Sbjct: 57 YKKPEQAQKALKQLQGHTVDGHKLEVRISER 87
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 55.5 bits (132), Expect = 9e-08, Method: Composition-based stats.
Identities = 29/83 (34%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
G+SG ++ LYVG L FN+T+ L +F G++ ++ + +D T RS GYG++ +++
Sbjct: 1 GSSG----SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSD 56
Query: 81 PADAARALDVLNFTPLNNKSIRI 103
A RAL+ LN L + +R+
Sbjct: 57 SECARRALEQLNGFELAGRPMRV 79
Score = 52.4 bits (124), Expect = 8e-07, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
LY+ +L +I ++ L+ +F FG I + +M+D +G SKG GF+ FS E A RAL ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 373 NGKMIVSKPLYVA 385
NG + +P+ V
Sbjct: 68 NGFELAGRPMRVG 80
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 267
+ ++V +L + T++ L+ IF +G I + V+M+D D G+SK +GF+ F +++ A +A+E
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 268 ALNGKKFDDREWYVGKAQKK 287
LNG + R VG ++
Sbjct: 66 QLNGFELAGRPMRVGHVTER 85
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQN 173
SG+ +++ +L +I L F FG I + + D +G+SKG+GF+ F + E A+
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 174 AIDKLNGMLINDKQVFVGH 192
A+++LNG + + + VGH
Sbjct: 63 ALEQLNGFELAGRPMRVGH 81
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
S++VG++ + T+ QL D+FS+VG V+S R+ D T + GYG+ Y + A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 91 LNFTPLNNKSIRI 103
LN + +++R+
Sbjct: 70 LNGREFSGRALRV 82
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 33/94 (35%), Positives = 51/94 (54%), Gaps = 2/94 (2%)
Query: 203 AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADD 261
A+ +VFV N+ T+E LK IF E G + S ++ D + GK K +GF +++ +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 262 AAKAVEALNGKKFDDREWYVGKAQKKSEREQELK 295
A A+ LNG++F R V A + +E ELK
Sbjct: 63 ALSAMRNLNGREFSGRALRVDNAASEKNKE-ELK 95
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 45/78 (57%), Gaps = 7/78 (8%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
++F+ N+ + L D FS G ++S ++ D +G+ KG+GF +++++E+A +A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 178 LNGMLINDKQVFVGHFLR 195
LNG + F G LR
Sbjct: 70 LNG------REFSGRALR 81
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: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
++++ N+ +E+LK++FSE G + S +++ D +G KG GF + E A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 372 MNGKMIVSKPLYV---AVAQRKEE 392
+NG+ + L V A + KEE
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEE 93
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
L++ LG DE ++++F FGTI C V+R P G SKG FV F T EA A+ +
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 373 NGKMIV---SKPLYVAVAQRKEE 392
+ + S L V A ++E
Sbjct: 74 HSSRTLPGASSSLVVKFADTEKE 96
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
+FV L + TDED++K+F +GTI V+R DG SK FV F+ +A A+ L
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 270 NGKK 273
+ +
Sbjct: 74 HSSR 77
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
+F+ L K + + F FG I C + G SKG FV+F+ AQ AI+ L
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 179 N 179
+
Sbjct: 74 H 74
>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: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
+ VFV NLD + LK++F G + A ++ D DGKS+ G V FE + +A +A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 269 LNGKKFDDREWYV 281
NG+ DR +V
Sbjct: 76 FNGQLLFDRPMHV 88
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 46/79 (58%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
G +++ NL + +KLKE+FS G + ++ D G S+G G V F EA +A++
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 371 EMNGKMIVSKPLYVAVAQR 389
NG+++ +P++V + +R
Sbjct: 75 MFNGQLLFDRPMHVKMDER 93
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
+F+ NLD + K L + FS G ++ I D G+S+G G V FE A AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 179 NGMLINDKQVFV 190
NG L+ D+ + V
Sbjct: 77 NGQLLFDRPMHV 88
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
L ++++V +LD+ V +L ++FS G V+ + D +S G G V + +A +A
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQA 72
Query: 88 LDVLNFTPLNNKSIRIMYSHR 108
+ + N L ++ + + R
Sbjct: 73 ISMFNGQLLFDRPMHVKMDER 93
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
++YVG LD V++ L++LF Q G V++ + +D T + GYG+V + + DA A+ +
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 91 LNFTPLNNKSIRI 103
++ L K IR+
Sbjct: 77 MDMIKLYGKPIRV 89
Score = 37.7 bits (86), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENK 168
P ++ +++ LD+ + L + F G +++ + D +GQ +G+GFV+F ++
Sbjct: 8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 169 ESAQNAIDKLNGMLINDKQVFV 190
E A AI ++ + + K + V
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRV 89
Score = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEA 365
++ Q +Y+ L + + + L ELF + G + + + +D +G +G GFV F + E+A
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 366 SRALAEMNGKMIVSKPLYV 384
A+ M+ + KP+ V
Sbjct: 71 DYAIKIMDMIKLYGKPIRV 89
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
V+V LDE ++ L ++F + G + + + +D G+ + +GFV F + +DA A++ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 270 NGKKFDDREWYVGKA 284
+ K + V KA
Sbjct: 78 DMIKLYGKPIRVNKA 92
>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 = 3e-07, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 1/86 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
N+ + + ++D L F +G I S KI D + QS+G+GFV+F++ SAQ AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 178 LNGMLINDKQVFVGHFLRKQERETVA 203
LNG I +K++ V +R +A
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIA 129
Score = 53.5 bits (127), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
NL + + ++D+ +L++LF +G I S K++ D + S+G GFV F + A +A+A
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 372 MNGKMIVSKPLYVAVAQRKEER 393
+NG I++K L VA+A +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 53/96 (55%), Gaps = 4/96 (4%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
+L V + V + QL LF + G + SV++ D TR+S GYG+V + + + A +A+
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 91 LNFTPLNNKSIRIMYS---HRDPSIRKS-GTGNIFI 122
LN + NK +++ + H+ P I + G GN ++
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAV 266
N+ V + + + L+++F YG I S ++ D + + S+ +GFV F++ A +A+
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 267 EALNGKKFDDREWYVGKAQKKSER 290
LNG ++ V A +R
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQR 125
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 53.1 bits (126), Expect = 4e-07, Method: Composition-based stats.
Identities = 29/95 (30%), Positives = 54/95 (56%), Gaps = 3/95 (3%)
Query: 19 AAGASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
++G+SG + T++ ++VGDL +T + F+ G++ RV +D++T +S GYG+
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGF 61
Query: 76 VNYANPADAARALDVLNFTPLNNKSIRIMYSHRDP 110
V++ N DA A+ + L + IR ++ R P
Sbjct: 62 VSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKP 96
Score = 51.6 bits (122), Expect = 1e-06, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
+VFV +L T ED+K F +G I+ A V++D GKSK +GFV+F N DA A+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 269 LNGKKFDDREWYVGKAQKK 287
+ G+ R+ A +K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
++F+ +L I + + F+ FG I ++ D +G+SKG+GFV F NK A+NAI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 178 LNGMLINDKQVFVGHFLRK 196
+ G + +Q+ RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 49/89 (55%), Gaps = 4/89 (4%)
Query: 303 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 361
K+T + F ++++ +L I E +K F+ FG I+ +V++D +G SKG GFV+F
Sbjct: 10 KDTSNHF---HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 362 PEEASRALAEMNGKMIVSKPLYVAVAQRK 390
+A A+ M G+ + + + A RK
Sbjct: 67 KLDAENAIVHMGGQWLGGRQIRTNWATRK 95
>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 = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 1/87 (1%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
+G NL+I +L D+ L ++F FG + S KV D + +SK GFV++ P A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRA 395
+ MNG I K L V + + K + ++
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSKNDSKS 110
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 268
N+F+ +L + D+DL ++F +G + SA V D SKCFGFV+++N A A+++
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 269 LNG 271
+NG
Sbjct: 87 MNG 89
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
N+FI +L + + L F FGN++S K+ D + SK FGFV ++N SAQ AI
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 178 LNGMLINDKQVFV 190
+NG I K++ V
Sbjct: 87 MNGFQIGMKRLKV 99
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L++ L D L +F G V+S +V D T S +G+V+Y NP A A+ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 92 NFTPLNNKSIRI 103
N + K +++
Sbjct: 88 NGFQIGMKRLKV 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: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
SG+ IF++NL K L D F+ G++L I + +G+SKG G V+FE+ E A+ A
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 61
Query: 175 IDKLNGMLINDKQVFV 190
+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: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
+ +FV+NL T + LK F E G + A + + +GKSK G V FE+ + A +A
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRM 64
Query: 269 LNGKKFDDRE 278
+NG K RE
Sbjct: 65 MNGMKLSGRE 74
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
++++NL + LK+ F+E G + + + +G SKG G V F +PE A RA MN
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 66
Query: 374 GKMIVSKPLYVAV 386
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: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAID-- 176
+FI L K L D FS FG ++ C + D +G+S+GFGFV F+ ES +D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 177 --KLNGMLINDKQ 187
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: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 371
++I L + LK+ FS+FG + C + DP +G S+G GFV F E + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 372 ---MNGKMIVSK 380
+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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE-- 267
+F+ L TT +DLK F ++G + + D G+S+ FGFV F+ ++ K ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 268 --ALNGKKFDDR 277
LNGK D +
Sbjct: 62 EHKLNGKVIDPK 73
Score = 36.6 bits (83), Expect = 0.044, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
+++G L ++ T L D FS+ G+V+ + D T RS G+G+V + + +D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 265
K N++V NL + TD+ L IFG+YG+I ++RD G+ + FV + ++A +A
Sbjct: 12 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 266 VEALN 270
+ 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: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
NLY+ NL +I D++L +F ++G+I ++RD +G +G FV ++ EEA A++
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 372 MNGKMIV--SKPLYVAVAQ 388
+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: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
N+++ NL ++I L F +G+I+ I D +G+ +G FV++ +E AQ AI
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 178 LNGML 182
LN ++
Sbjct: 75 LNNVI 79
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 20 AGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA 79
A G T+LYV +L +TD QL +F + G ++ + RD T R G +V Y
Sbjct: 4 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 63
Query: 80 NPADAARALDVLN 92
+A A+ LN
Sbjct: 64 KREEAQEAISALN 76
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
N+++ L K++ K + FS +G I++ +I D +G S+G GF++F+ + A+ AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 178 LNG 180
LNG
Sbjct: 63 LNG 65
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 46/74 (62%), Gaps = 5/74 (6%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
NLY+ L ++ +++++LFS++G I + +++ D +G+S+G GF+ F EA A+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 372 MNGKMIVSKPLYVA 385
+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: 210 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
N++V L ++ + ++++++F +YG ITS +++ G S+ GF+ F+ +A +A++
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 269 LNGKK 273
LNG+K
Sbjct: 63 LNGQK 67
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
+LYV L ++ ++ LFSQ G++++ R+ D +T S G G++ + +A A+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 91 LN 92
LN
Sbjct: 63 LN 64
>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 = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 46/187 (24%), Positives = 85/187 (45%), Gaps = 18/187 (9%)
Query: 211 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 264
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ------AMKETVDKFQGLNLYIKN 318
A+ A +G F + + ++ Q L G E + TV L+I
Sbjct: 67 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121
Query: 319 LGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMI 377
L + ++D+++KEL + FG + + +++D +G+SKG F + +A+A +NG +
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
Query: 378 VSKPLYV 384
K L V
Sbjct: 182 GDKKLLV 188
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 44/189 (23%), Positives = 83/189 (43%), Gaps = 37/189 (19%)
Query: 32 LYVGDLDFNVTDSQLYDLFS---QVG--------QVLSVRVCRDLSTRRSLGYGYVNYAN 80
LYVG++ F +T+ + D F+ ++G VL+V++ +D ++ + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVD 62
Query: 81 PADAARALDVLNFTPLNNKSIRIMYSH---------RDPSIRKSGT---------GNIFI 122
A A D + F +S++I H +PS+ G +FI
Sbjct: 63 ETTQAMAFDGIIF---QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 123 KNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGM 181
L ++ + + +SFG + + + D +G SKG+ F ++ + AI LNGM
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Query: 182 LINDKQVFV 190
+ DK++ V
Sbjct: 180 QLGDKKLLV 188
>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 = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
+ +LYVG+L F T+ Q+Y+LFS+ G + + + D + + G+ +V Y + ADA A+
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAM 76
Query: 89 DVLNFTPLNNKSIR 102
+N T L+++ IR
Sbjct: 77 RYINGTRLDDRIIR 90
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 192 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 251
HF E + +K K ++V NL TT+E + ++F + G I ++ D + F
Sbjct: 3 HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF 61
Query: 252 GFVNFENADDAAKAVEALNGKKFDDR----EWYVG 282
FV + + DA A+ +NG + DDR +W G
Sbjct: 62 CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 96
Score = 37.7 bits (86), Expect = 0.019, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 112 IRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESA 171
++KS T +++ NL + +++ FS G+I + D + GF FV++ ++ A
Sbjct: 15 LKKSCT--LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADA 72
Query: 172 QNAIDKLNGMLINDK 186
+NA+ +NG ++D+
Sbjct: 73 ENAMRYINGTRLDDR 87
Score = 32.3 bits (72), Expect = 0.83, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 291 EQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI 350
+Q +G E+ +E + K + LY+ NL +E++ ELFS+ G I + D
Sbjct: 1 DQHFRGDNEE--QEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT 57
Query: 351 SKGSGFVAFSTPEEASRALAEMNG 374
+ G FV + + +A A+ +NG
Sbjct: 58 ACGFCFVEYYSRADAENAMRYING 81
>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: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 271
V L TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 272 KKFDDREWYV 281
+ D R V
Sbjct: 111 MELDGRRIRV 120
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 48/104 (46%), Gaps = 5/104 (4%)
Query: 8 HQAQMSGPNGVAAGAS-----GNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVC 62
H A M+G + G+ N L V L T+ L ++FS+ G + V +
Sbjct: 20 HMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79
Query: 63 RDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYS 106
D +RRS G+ +V + N DA A + N L+ + IR+ +S
Sbjct: 80 YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 132 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
+ L + FS +G I I D S +S+GF FV FEN + A+ A ++ NGM ++ +++ V
Sbjct: 61 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 53 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 370 AEMNG 374
NG
Sbjct: 106 ERANG 110
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 21/171 (12%)
Query: 32 LYVGDLDFNVTDSQLYDLFS---QVG--------QVLSVRVCRDLSTRRSLGYGYVNYAN 80
LYVG++ F +T+ + D F+ ++G VL+V++ +D ++ + +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVD 64
Query: 81 PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSS 140
A A D + F +S++I H + G +FI L ++ + + +S
Sbjct: 65 ETTQAMAFDGIIF---QGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTS 119
Query: 141 FGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
FG + + + D +G SKG+ F ++ + AI LNGM + DK++ V
Sbjct: 120 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
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: 211 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 264
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 324
A+ A +G F + + ++ Q L G + L+I L + ++
Sbjct: 69 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 109
Query: 325 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 383
D+++KEL + FG + + +++D +G+SKG F + +A+A +NG + K L
Sbjct: 110 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 169
Query: 384 V 384
V
Sbjct: 170 V 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 21/171 (12%)
Query: 32 LYVGDLDFNVTDSQLYDLFS---QVG--------QVLSVRVCRDLSTRRSLGYGYVNYAN 80
LYVG++ F +T+ + D F+ ++G VL+V++ +D ++ + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVD 62
Query: 81 PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSS 140
A A D + F +S++I H + G +FI L ++ + + +S
Sbjct: 63 ETTQAMAFDGIIF---QGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTS 117
Query: 141 FGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
FG + + + D +G SKG+ F ++ + AI LNGM + DK++ V
Sbjct: 118 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
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: 211 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 264
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 324
A+ A +G F + + ++ Q L G + L+I L + ++
Sbjct: 67 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 107
Query: 325 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 383
D+++KEL + FG + + +++D +G+SKG F + +A+A +NG + K L
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Query: 384 V 384
V
Sbjct: 168 V 168
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 50/242 (20%), Positives = 103/242 (42%), Gaps = 20/242 (8%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+ + L +VT+ +++DL S ++ C + G +V N A A++
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAF 77
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIA 150
+ + L + + + D + + NL S+ + + FG++ C +
Sbjct: 78 HQSRLRERELSVQLQPTD--------ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129
Query: 151 TDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNN 210
++ +GQSKG+GF ++ K+SA A L G + + ++V H+ + + ++
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSR--C 186
Query: 211 VFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
+ V L D D L + + T + DG+ K F + +E A+ A +A +
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 270 NG 271
+G
Sbjct: 247 DG 248
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 40/163 (24%), Positives = 71/163 (43%), Gaps = 6/163 (3%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L V +L ++T Q +L G + + T +S GYG+ Y AARA L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 92 NFTPLNNKSIRIMYS---HRDPSIRKSGTGNIFIKNLDKSI-DHKALHDTFSSFGNILSC 147
PL +++ + ++ P++ S + + L D AL S+ + C
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 148 KIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
++A GQ KGF +++E E A+ A + +G+ + + V
Sbjct: 216 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 271 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 330
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 79 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 114
Query: 331 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 384
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>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 = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 50/242 (20%), Positives = 103/242 (42%), Gaps = 20/242 (8%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+ + L +VT+ +++DL S ++ C + G +V N A A++
Sbjct: 23 ILIRGLPGDVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAF 75
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIA 150
+ + L + + + D + + NL S+ + + FG++ C +
Sbjct: 76 HQSRLRERELSVQLQPTD--------ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 127
Query: 151 TDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNN 210
++ +GQSKG+GF ++ K+SA A L G + + ++V H+ + + ++
Sbjct: 128 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSR--C 184
Query: 211 VFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
+ V L D D L + + T + DG+ K F + +E A+ A +A +
Sbjct: 185 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 244
Query: 270 NG 271
+G
Sbjct: 245 DG 246
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 40/163 (24%), Positives = 71/163 (43%), Gaps = 6/163 (3%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L V +L ++T Q +L G + + T +S GYG+ Y AARA L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 92 NFTPLNNKSIRIMYS---HRDPSIRKSGTGNIFIKNLDKSI-DHKALHDTFSSFGNILSC 147
PL +++ + ++ P++ S + + L D AL S+ + C
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 213
Query: 148 KIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
++A GQ KGF +++E E A+ A + +G+ + + V
Sbjct: 214 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 256
Score = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 23 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 76
Query: 271 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 330
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 77 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 112
Query: 331 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 384
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 113 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
>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 = 3e-06, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
SG IF++NL K L D F+ G++L I + +G+SKG G V+FE+ E A+ A
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 64
Query: 175 IDKLNGMLINDKQVFV 190
+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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+FV+NL T + LK F E G + A + + +GKSK G V FE+ + A +A +N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 271 GKKFDDRE 278
G K RE
Sbjct: 70 GMKLSGRE 77
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
++++NL + LK+ F+E G + + + +G SKG G V F +PE A RA MN
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 374 GKMIVSKPLYVAV 386
G + + + V +
Sbjct: 70 GMKLSGREIDVRI 82
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 50/242 (20%), Positives = 103/242 (42%), Gaps = 20/242 (8%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+ + L +VT+ +++DL S ++ C + G +V N A A++
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAF 77
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSC-KIA 150
+ + L + + + D + + NL S+ + + FG++ C +
Sbjct: 78 HQSRLRERELSVQLQPTD--------ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129
Query: 151 TDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNN 210
++ +GQSKG+GF ++ K+SA A L G + + ++V H+ + + ++
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSR--C 186
Query: 211 VFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
+ V L D D L + + T + DG+ K F + +E A+ A +A +
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 270 NG 271
+G
Sbjct: 247 DG 248
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 40/163 (24%), Positives = 71/163 (43%), Gaps = 6/163 (3%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L V +L ++T Q +L G + + T +S GYG+ Y AARA L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 92 NFTPLNNKSIRIMYS---HRDPSIRKSGTGNIFIKNLDKSI-DHKALHDTFSSFGNILSC 147
PL +++ + ++ P++ S + + L D AL S+ + C
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 148 KIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
++A GQ KGF +++E E A+ A + +G+ + + V
Sbjct: 216 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 271 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 330
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 79 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 114
Query: 331 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 384
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
+++ NL + +E L ELF + G +T + +D G K GFV F PE S A+A +N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 374 GKMIVSKPLYVA 385
G + +P+ V+
Sbjct: 79 GIRLYGRPINVS 90
Score = 48.9 bits (115), Expect = 7e-06, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 39/67 (58%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
VFV NL+ +E L ++F + G +T + +D +GK K FGFV F++ + + A+ LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 271 GKKFDDR 277
G + R
Sbjct: 79 GIRLYGR 85
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F+ NL+ + + L++ F G + I D G+ K FGFV F++ ES AI LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 180 GMLINDKQVFV 190
G+ + + + V
Sbjct: 79 GIRLYGRPINV 89
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
+++VG+L+ V + LY+LF Q G + V +C+D + +G+V + +P + A+ +
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK-SFGFVCFKHPESVSYAIAL 76
Query: 91 LNFTPLNNKSIRI 103
LN L + I +
Sbjct: 77 LNGIRLYGRPINV 89
>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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 271 GKKFDDR 277
G D R
Sbjct: 91 GVPLDGR 97
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 374 GKMIVSKPLYV 384
G + +P+ +
Sbjct: 91 GVPLDGRPMNI 101
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L V +LDF V+D+ + +LF++ G + V D S RSLG V++ ADA +A+
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKAMKQY 89
Query: 92 NFTPLNNKSIRI 103
N PL+ + + I
Sbjct: 90 NGVPLDGRPMNI 101
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+ + NLD + + + F+ FG + + D SG+S G V FE K A A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 180 GMLIN 184
G+ ++
Sbjct: 91 GVPLD 95
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDRE 278
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 83
Query: 279 WYV 281
V
Sbjct: 84 IRV 86
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 42/86 (48%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
G+ N L V L T+ L ++FS+ G + V + D +RRS G+ +V + N
Sbjct: 4 GSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 81 PADAARALDVLNFTPLNNKSIRIMYS 106
DA A + N L+ + IR+ +S
Sbjct: 64 VDDAKEAKERANGMELDGRRIRVDFS 89
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 132 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
+ L + FS +G I I D S +S+GF FV FEN + A+ A ++ NGM ++ +++ V
Sbjct: 27 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 86
Query: 191 GHFLRKQ 197
+ K+
Sbjct: 87 DFSITKR 93
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 19 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 370 AEMNG 374
NG
Sbjct: 72 ERANG 76
>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 = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 64/269 (23%), Positives = 116/269 (43%), Gaps = 21/269 (7%)
Query: 25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
N+ LTT L V +L + +++Y F G ++ V V L +++ + + +A A
Sbjct: 38 NRELTTVL-VKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGA 94
Query: 85 ARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
A+ + N+ I+ SH ++ N S + + D +
Sbjct: 95 LAAITKTHKVVGQNE---IIVSHLTEC-------TLWXTNFPPSYTQRNIRDLLQDINVV 144
Query: 145 -LSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVF--VGHFLRKQERET 201
LS ++ + S+ F ++ +KE A+ ++KLNG+ I + V + L K +R T
Sbjct: 145 ALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKR-T 203
Query: 202 VAIKTKFNNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKS--KCFGFVNFEN 258
+ + + ++NL DE+ L++ F +G+I + S C F FEN
Sbjct: 204 DSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFEN 263
Query: 259 ADDAAKAVEALNGKKFDDREWYVGKAQKK 287
D A +A++ N +RE V A KK
Sbjct: 264 KDSAERALQX-NRSLLGNREISVSLADKK 291
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 205 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
K++ + V N+ D DL+++FG++G I ++ + G SK FGFV FEN+ DA +
Sbjct: 26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADR 84
Query: 265 AVEALNGKKFDDREWYVGKAQKK 287
A E L+G + R+ V A +
Sbjct: 85 AREKLHGTVVEGRKIEVNNATAR 107
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 9/80 (11%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+V ++ F D L +F Q G++L V + + R S G+G+V + N ADA RA + L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKL 89
Query: 92 NFT-------PLNNKSIRIM 104
+ T +NN + R+M
Sbjct: 90 HGTVVEGRKIEVNNATARVM 109
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 114 KSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQN 173
KS + + N+ L F FG IL +I + G SKGFGFV FEN A
Sbjct: 26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADR 84
Query: 174 AIDKLNGMLINDKQVFV 190
A +KL+G ++ +++ V
Sbjct: 85 AREKLHGTVVEGRKIEV 101
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 305 TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE 364
T +K Q L++ N+ D L+++F +FG I +++ + G SKG GFV F +
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSAD 81
Query: 365 ASRALAEMNGKMIVSKPLYV 384
A RA +++G ++ + + V
Sbjct: 82 ADRAREKLHGTVVEGRKIEV 101
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDRE 278
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 279 WYV 281
V
Sbjct: 87 IRV 89
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 3/91 (3%)
Query: 19 AAGASGNQF---LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
++G+SGN+ L V L T+ L ++FS+ G + V + D +RRS G+ +
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 76 VNYANPADAARALDVLNFTPLNNKSIRIMYS 106
V + N DA A + N L+ + IR+ +S
Sbjct: 62 VYFENVDDAKEAKERANGMELDGRRIRVDFS 92
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 132 KALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
+ L + FS +G I I D S +S+GF FV FEN + A+ A ++ NGM ++ +++ V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Query: 191 GHFLRKQ 197
+ K+
Sbjct: 90 DFSITKR 96
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 22 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 370 AEMNG 374
NG
Sbjct: 75 ERANG 79
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/85 (38%), Positives = 48/85 (56%), Gaps = 6/85 (7%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSC---KVMRDPSGISKGSGFVAFSTPEEASRAL 369
+L++ +L +DD L E F + SC KV+ D +G+SKG GFV F+ E RAL
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVK--VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
Query: 370 AEMNGKM-IVSKPLYVAVAQRKEER 393
E G + + SKP+ ++VA K R
Sbjct: 69 TECQGAVGLGSKPVRLSVAIPKASR 93
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQV-GQVLSVRVCRDLSTRRSLGYGYVNYA 79
G+SG+ SL+VGDL +V D LY+ F +V +V D T S GYG+V +
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFT 59
Query: 80 NPADAARAL-DVLNFTPLNNKSIRI 103
+ + RAL + L +K +R+
Sbjct: 60 DELEQKRALTECQGAVGLGSKPVRL 84
Score = 35.4 bits (80), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSS-FGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
++F+ +L +D L++ F + + K+ D +G SKG+GFV+F ++ + A+ +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 178 LNGML 182
G +
Sbjct: 71 CQGAV 75
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 220 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDRE 278
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 279 WYV 281
V
Sbjct: 87 IRV 89
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 3/88 (3%)
Query: 19 AAGASGNQF---LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
++G+SGN+ L V L T+ L ++FS+ G + V + D +RRS G+ +
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 76 VNYANPADAARALDVLNFTPLNNKSIRI 103
V + N DA A + N L+ + IR+
Sbjct: 62 VYFENVDDAKEAKERANGMELDGRRIRV 89
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 131 HKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVF 189
+ L + FS +G I I D S +S+GF FV FEN + A+ A ++ NGM ++ +++
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 190 V 190
V
Sbjct: 89 V 89
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 369
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 22 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 370 AEMNGKMIVSKPLYVA 385
NG + + + V+
Sbjct: 75 ERANGMELDGRRIRVS 90
>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 = 5e-06, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L++ L +E + LF FG I C V+R P G SKG FV FS+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 374 GKMIV---SKPLYVAVAQRKEE 392
G + S L V A +E
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+FV L++ ++ED+ ++F +G I V+R DG SK FV F + +A A+ AL+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 271 GKK 273
G +
Sbjct: 78 GSQ 80
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F+ L+K + + F FG I C + G SKG FV+F + AQ AI L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 180 G 180
G
Sbjct: 78 G 78
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
+FV+NL ++++EDL+K+F YG ++ D K K F FV F + A KA +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 270 NGKKFDDREWYVGKAQKKSEREQ 292
+G+ F R +V + K E Q
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQ 93
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
L+++NL + +E L++LFS +G ++ D + KG FV F PE A +A AE+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 373 NGKMIVSKPLYVAVAQRKEE 392
+G++ + L+V + K+E
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
Score = 35.4 bits (80), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+F++NL + + L FS++G + D + + KGF FV F E A A ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 179 NGMLINDKQVFVGHFLR 195
+G QVF G L
Sbjct: 71 DG------QVFQGRMLH 81
Score = 32.0 bits (71), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
L+V +L + ++ L LFS G + + D T++ G+ +V + P A +A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 54/90 (60%), Gaps = 11/90 (12%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L+++NL +++ +E L++ FS+FG + K ++D + F+ F + A +A+ EMN
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYA-------FIHFDERDGAVKAMEEMN 66
Query: 374 GKMIVSKPLYVAVA----QRKEERRARLQA 399
GK + + + + A Q+++ER+A+ QA
Sbjct: 67 GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 50/96 (52%), Gaps = 7/96 (7%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
K +FV+NL + T+E L+K F ++G + ++D + F++F+ D A KA
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKA 61
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQA 301
+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: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F++NL ++ + L FS FG + K D + F+ F+ ++ A A++++N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 180 G 180
G
Sbjct: 67 G 67
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 47/96 (48%), Gaps = 10/96 (10%)
Query: 21 GASGNQFL--TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNY 78
G+SG+ + L+V +L VT+ L FSQ G++ V+ +D Y ++++
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52
Query: 79 ANPADAARALDVLNFTPLNNKSIRIMYSHRDPSIRK 114
A +A++ +N L ++I I+++ RK
Sbjct: 53 DERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRK 88
>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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 271 GKKFDDR 277
G D R
Sbjct: 92 GVPLDGR 98
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 374 GKMIVSKP 381
G + +P
Sbjct: 92 GVPLDGRP 99
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L V +LDF V+D+ + +LF++ G + V D S RSLG V++ ADA +A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG-RSLGTADVHFERKADALKAXKQY 90
Query: 92 NFTPLNNKSIRI 103
N PL+ + I
Sbjct: 91 NGVPLDGRPXNI 102
Score = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+ + NLD + + + F+ FG + + D SG+S G V FE K A A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 180 GMLIN 184
G+ ++
Sbjct: 92 GVPLD 96
>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 = 7e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 272
V N+ D DL+++FG++G I ++ + G SK FGFV FEN+ DA +A E L+G
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 273 KFDDREWYVGKAQKK 287
+ R+ V A +
Sbjct: 79 VVEGRKIEVNNATAR 93
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 9/80 (11%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+V ++ F D L +F Q G++L V + + R S G+G+V + N ADA RA + L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKL 75
Query: 92 NFT-------PLNNKSIRIM 104
+ T +NN + R+M
Sbjct: 76 HGTVVEGRKIEVNNATARVM 95
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 134 LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
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: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L++ N+ D L+++F +FG I +++ + G SKG GFV F +A RA +++
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 374 GKMIVSKPLYV 384
G ++ + + V
Sbjct: 77 GTVVEGRKIEV 87
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 21 GASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVN 77
G+SG+ + T+ LYVG L V D L+ F G + +++ D T + G+ +V
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 78 YANPADAARALDVLNFTPLNNKSIRI 103
+ DAA A+D +N + L ++IR+
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRV 86
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 179 N 179
N
Sbjct: 75 N 75
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 373 NGKMIVSKPLYVAVAQ 388
N + + + V +A+
Sbjct: 75 NESELFGRTIRVNLAK 90
Score = 35.8 bits (81), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 269
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 270 NGKKFDDREWYVGKAQ 285
N + R V A+
Sbjct: 75 NESELFGRTIRVNLAK 90
>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 = 48.9 bits (115), Expect = 9e-06, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F+ +D +D + F+ +G++ KI TD +G SKG+GFV F N Q ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTK 207
+ + K++ +G +RKQ T ++ +
Sbjct: 70 QINFHGKKLKLGPAIRKQNLSTYHVQPR 97
Score = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 269 ---LNGKKF 274
+GKK
Sbjct: 70 QINFHGKKL 78
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 31/46 (67%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 359
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 37.7 bits (86), Expect = 0.019, Method: Composition-based stats.
Identities = 23/90 (25%), Positives = 50/90 (55%), Gaps = 10/90 (11%)
Query: 26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAA 85
+ + +++VG +D + ++++ F++ G V V++ D T S GYG+V++ N D
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQ 64
Query: 86 RALDV-LNFTPLNNKSIRIMYSHRDPSIRK 114
+ ++ +NF + K +++ P+IRK
Sbjct: 65 KIVESQINF---HGKKLKL-----GPAIRK 86
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.9 bits (115), Expect = 9e-06, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 267
+ V+V NL S T+ DL +IF +YG + +M+D D KSK F+ F + D A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 268 ALNGKKFDDR 277
A+N K+ R
Sbjct: 77 AINNKQLFGR 86
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
+++YV +L F++T++ LY +FS+ G+V+ V + +D TR+S G ++ + + A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 90 VLNFTPLNNKSIR 102
+N L + I+
Sbjct: 77 AINNKQLFGRVIK 89
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
+++ NL S+ + L+ FS +G ++ I D + +SKG F+ F +K+SAQN
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA- 77
Query: 179 NGMLINDKQVF 189
IN+KQ+F
Sbjct: 78 ----INNKQLF 84
Score = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
+Y+ NL S+ + L +FS++G + +M+D + SKG F+ F + A +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 373 NGKMIVSKPLYVAVA 387
N K + + + ++A
Sbjct: 79 NNKQLFGRVIKASIA 93
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
++YVG+L ++ T Q+ +LFSQ G+V +V++ D T++ G+G+V + + A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61
Query: 91 LNFTPLNNKSIRIMYSHRDPSI 112
L+ T ++IR+ ++ S+
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSL 83
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: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
N+Y+ NL S E++KELFS+FG + + K++ D + KG GFV E S A+A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 372 MNGKMIVSKPLYVAVAQRKE 391
++ + + + 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: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
NI++ NL S + + + FS FG + + K+ D + + KGFGFV+ + +ES AI K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 178 LNGMLINDKQVFVGHFLRKQE 198
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: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEA 268
N++V NL S T E +K++F ++G + + ++ D + K K FGFV + + ++A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 269 LNGKKFDDREWYVGKAQKKSERE 291
L+ F R V +A K E
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLE 84
>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 = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFEN 167
+ S + G F+ L K L D F+ FG ++ C I D +G+S+GFGF+ F++
Sbjct: 3 NASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
Query: 168 KESAQNAID----KLNGMLINDKQ 187
S + +D +L+G +I+ K+
Sbjct: 63 AASVEKVLDQKEHRLDGRVIDPKK 86
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 37/68 (54%)
Query: 22 ASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP 81
AS N+ +VG L ++ + L D F++ G+V+ + D +T RS G+G++ + +
Sbjct: 4 ASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDA 63
Query: 82 ADAARALD 89
A + LD
Sbjct: 64 ASVEKVLD 71
Score = 36.6 bits (83), Expect = 0.039, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 212 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA-- 268
FV L T+ +DLK F ++G + + D + G+S+ FGF+ F++A K ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 269 --LNGKKFDDRE 278
L+G+ D ++
Sbjct: 75 HRLDGRVIDPKK 86
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 315 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE-- 371
++ L + LK+ F++FG + C + DP +G S+G GF+ F + L +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 372 --MNGKMIVSK 380
++G++I K
Sbjct: 75 HRLDGRVIDPK 85
>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 = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 511 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 567
R LGE LYP V+ ++ A+K+TGMLLE+ ++L LL S ++L+A+V EAME++
Sbjct: 6 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEEAMELI 62
>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: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNG 271
V NL E T + DL+++F +G+I+ + +D G+SK F F++F +DAA+A+ ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 272 KKFD 275
+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: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGS-GQSKGFGFVQFENK 168
P+ R I + NL + L + F FG+I +A D + GQSKGF F+ F +
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 169 ESAQNAIDKLNG 180
E A AI ++G
Sbjct: 68 EDAARAIAGVSG 79
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 316 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEMNG 374
+ NL + + L+ELF FG+I+ + +D + G SKG F++F E+A+RA+A ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Score = 33.9 bits (76), Expect = 0.24, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 13 SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
SGPN A ++ V +L + ++ L +LF G + + + +D +T +S G
Sbjct: 6 SGPNRRADD-------NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG 58
Query: 73 YGYVNYANPADAARAL 88
+ ++++ DAARA+
Sbjct: 59 FAFISFHRREDAARAI 74
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 511 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 567
R LGE LYP V+ ++ A+K+TGMLLE+ ++L LL S ++L+A+V EAME++
Sbjct: 1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELI 57
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 194 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFG 252
L +++RE K +F +F+ L TT+E L+ + ++G +T VVMRD +S+ FG
Sbjct: 17 LERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
Query: 253 FVNFENADDAAKAVEA 268
FV F + + A+ A
Sbjct: 73 FVTFSSMAEVDAAMAA 88
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 5/79 (6%)
Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
+K Q L+I L +E L+ + ++G +T C VMRDP S S+G GFV FS+ E
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 366 SRALA----EMNGKMIVSK 380
A+A ++G+++ K
Sbjct: 83 DAAMAARPHSIDGRVVEPK 101
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 35/57 (61%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
L++G L F T+ L + + Q G++ V RD +++RS G+G+V +++ A+ A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI-- 175
+FI L ++L + + +G + C + D S +S+GFGFV F + A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 176 --DKLNGMLINDKQV 188
++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: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 271
V NL T+ + L+++F +YG + + RD K S+ F FV F + DA A++A++G
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 272 KKFDDREWYVGKAQ 285
D RE V A+
Sbjct: 112 AVLDGRELRVQMAR 125
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
TSL V +L + + L +F + G+V V + RD T+ S G+ +V + + DA A+D
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 90 VLNFTPLNNKSIRI 103
++ L+ + +R+
Sbjct: 108 AMDGAVLDGRELRV 121
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: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 174
G ++ + NL L F +G + I D + +S+GF FV+F +K A++A
Sbjct: 46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105
Query: 175 IDKLNGMLINDKQVFV 190
+D ++G +++ +++ V
Sbjct: 106 MDAMDGAVLDGRELRV 121
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
+L + NL + L+ +F ++G + + RD + S+G FV F +A A+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 372 MNGKMIVSKPLYVAVAQ 388
M+G ++ + L V +A+
Sbjct: 109 MDGAVLDGRELRVQMAR 125
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L++ L ++ ++ LF FG I C ++R P G SKG FV +S+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 374 GKMIV---SKPLYVAVAQRKEE 392
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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+FV L++ +++D++++F +G I ++R DG SK FV + + +A A+ AL+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 271 GKK 273
G +
Sbjct: 78 GSQ 80
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKE 169
PS RK +F+ L+K + F +FGNI C I G SKG FV++ +
Sbjct: 13 PSHRK-----LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHA 67
Query: 170 SAQNAIDKLNG 180
AQ AI+ L+G
Sbjct: 68 EAQAAINALHG 78
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 179 N 179
N
Sbjct: 126 N 126
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 38/72 (52%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LYVG L V D L+ F G + +++ D T + G+ +V + DAA A+D +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 92 NFTPLNNKSIRI 103
N + L ++IR+
Sbjct: 126 NESELFGRTIRV 137
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: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 373 NGKMIVSKPLYVAVA 387
N + + + V +A
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 269
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 270 N 270
N
Sbjct: 126 N 126
>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 = 4e-05, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F+ +D +D + F+ +G++ KI TD +G SKG+GFV F N Q ++ +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 180 GMLINDKQVFVGHFLRKQ 197
+ + K++ +G +RKQ
Sbjct: 70 QINFHGKKLKLGPAIRKQ 87
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 269 ---LNGKKF 274
+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: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 359
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 23/90 (25%), Positives = 50/90 (55%), Gaps = 10/90 (11%)
Query: 26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAA 85
+ + +++VG +D + ++++ F++ G V V++ D T S GYG+V++ N D
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQ 64
Query: 86 RALDV-LNFTPLNNKSIRIMYSHRDPSIRK 114
+ ++ +NF + K +++ P+IRK
Sbjct: 65 KIVESQINF---HGKKLKL-----GPAIRK 86
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F+ +D +D + F+ +G++ KI TD +G SKG+GFV F N Q ++ +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 70
Query: 180 GMLINDKQVFVGHFLRKQ 197
+ + K++ +G +RKQ
Sbjct: 71 QINFHGKKLKLGPAIRKQ 88
Score = 45.8 bits (107), Expect = 6e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 269 ---LNGKKF 274
+GKK
Sbjct: 71 QINFHGKKL 79
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 31/46 (67%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 359
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
Score = 37.0 bits (84), Expect = 0.027, Method: Composition-based stats.
Identities = 23/90 (25%), Positives = 50/90 (55%), Gaps = 10/90 (11%)
Query: 26 QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAA 85
+ + +++VG +D + ++++ F++ G V V++ D T S GYG+V++ N D
Sbjct: 7 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQ 65
Query: 86 RALDV-LNFTPLNNKSIRIMYSHRDPSIRK 114
+ ++ +NF + K +++ P+IRK
Sbjct: 66 KIVESQINF---HGKKLKL-----GPAIRK 87
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 271 GKKFDDR 277
G D R
Sbjct: 151 GVPLDGR 157
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
Query: 371 EMNGKMIVSKPLYV 384
+ G + +P+ +
Sbjct: 148 QYKGVPLDGRPMDI 161
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 20 AGASGNQFLTTS--LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVN 77
+G G + + T L V +LDF V+D+ + +LF++ G + V D S RSLG V+
Sbjct: 77 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVH 135
Query: 78 YANPADAARALDVLNFTPLNNKSIRI 103
+ ADA +A+ PL+ + + I
Sbjct: 136 FERRADALKAMKQYKGVPLDGRPMDI 161
Score = 36.2 bits (82), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+ + NLD + + + F+ FG + + D SG+S G V FE + A A+ +
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 180 GMLINDKQVFV 190
G+ ++ + + +
Sbjct: 151 GVPLDGRPMDI 161
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 48/86 (55%), Gaps = 3/86 (3%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LY+ +L + +T ++YD+F + G + +RV TR G YV Y + DA A+D L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAVDHL 67
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSGT 117
+ ++N+ + ++Y + + + +K T
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQKMDT 93
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 28/117 (23%), Positives = 58/117 (49%), Gaps = 16/117 (13%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
++I+NL I + ++D F +G I ++ + +++G +V +E+ A+NA+D L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT 236
G ++++ + V ++ N F K +D +E LK + +YG T
Sbjct: 69 GFNVSNRYLVVLYY-------------NANRAFQK-MDTKKKEEQLKLLKEKYGINT 111
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A+ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHLS 68
Query: 374 GKMIVSKPLYV 384
G + ++ L V
Sbjct: 69 GFNVSNRYLVV 79
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+FVK L E TT+E LK+ F G++ + +V G SK FGFV+F + +DA A EA+
Sbjct: 18 LFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 271 GKKFD 275
+ D
Sbjct: 76 DGEID 80
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENK 168
P+ R + +F+K L + + L + SF + +I TD +G SKGFGFV F ++
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVDFNSE 64
Query: 169 ESAQNAIDKLNGMLINDKQV 188
E A+ A + + I+ +V
Sbjct: 65 EDAKAAKEAMEDGEIDGNKV 84
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L++K L + +E LKE F G++ + V +G SKG GFV F++ E+A A M
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 374 GKMIVSKPLYVAVAQRK 390
I + + A+ K
Sbjct: 76 DGEIDGNKVTLDWAKPK 92
>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 = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 58/138 (42%), Gaps = 14/138 (10%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L Y +FSQ GQ+L + V R L R G +V + + A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILS 146
AL + P +K +RI Y+ D I G ++ + +T +
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQET-------PA 120
Query: 147 CKIATDGSGQSKGFGFVQ 164
K A G G + G VQ
Sbjct: 121 TKKAVQGGGATPVVGAVQ 138
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 401
M G KP+ + A+ + A+++ F
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF ++G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA--FVIFKEVSSATN 67
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 298
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANP-------ADA 84
L+VG LD++ T L FSQ G+V+ + +D +T +S G+G+V + +P A
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 85 ARALDVLNFTP 95
LD N P
Sbjct: 79 PHTLDGRNIDP 89
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 265
+ +FV LD STT E L+ F +YG + V+M+D +S+ FGFV F++ +
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 266 VEA----LNGKKFDDR 277
+ + L+G+ D +
Sbjct: 75 LASRPHTLDGRNIDPK 90
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 118 GNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 167
G +F+ LD S + L FS +G ++ C I D + QS+GFGFV+F++
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Score = 42.0 bits (97), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 371
L++ L S E L+ FS++G + C +M+D + S+G GFV F P LA
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 372 ---MNGKMIVSKP 381
++G+ I KP
Sbjct: 79 PHTLDGRNIDPKP 91
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 267
+ ++++ L TTD+DL K+ YG I S + D K K +GFV+F++ A KAV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 268 AL 269
AL
Sbjct: 66 AL 67
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
G+SG ++ LY+ L TD L L G+++S + D +T + GYG+V++ +
Sbjct: 1 GSSG----SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS 56
Query: 81 PADAARALDVL 91
P+ A +A+ L
Sbjct: 57 PSAAQKAVTAL 67
Score = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQN 173
SG+ ++I+ L + L +G I+S K D + + KG+GFV F++ +AQ
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 174 AIDKL 178
A+ L
Sbjct: 63 AVTAL 67
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L Y +FSQ GQ+L + V R L R G +V + + A
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 401
M G KP+ + A+ + A+++ F
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF ++G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA--FVIFKEVSSATN 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 298
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>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 = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 179 N 179
N
Sbjct: 65 N 65
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 38/72 (52%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LYVG L V D L+ F G + +++ D T + G+ +V + DAA A+D +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 92 NFTPLNNKSIRI 103
N + L ++IR+
Sbjct: 65 NESELFGRTIRV 76
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 373 NGKMIVSKPLYVAVA 387
N + + + V +A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 35.8 bits (81), Expect = 0.063, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 269
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 270 N 270
N
Sbjct: 65 N 65
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 271 GKKFDDR 277
G D R
Sbjct: 98 GVPLDGR 104
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 371 EMNGKMIVSKPLYV 384
+ G + +P+ +
Sbjct: 95 QYKGVPLDGRPMDI 108
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 20 AGASGNQFLTTS--LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVN 77
+G G + + T L V +LDF V+D+ + +LF++ G + V D S RSLG V+
Sbjct: 24 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVH 82
Query: 78 YANPADAARALDVLNFTPLNNKSIRI 103
+ ADA +A+ PL+ + + I
Sbjct: 83 FERRADALKAMKQYKGVPLDGRPMDI 108
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+ + NLD + + + F+ FG + + D SG+S G V FE + A A+ +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 180 GMLIN 184
G+ ++
Sbjct: 98 GVPLD 102
>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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 271 GKKFDDR 277
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: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 370
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 371 EMNGKMIVSKPLYV 384
+ G + +P+ +
Sbjct: 95 QYKGVPLDGRPMDI 108
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 20 AGASGNQFLTTS--LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVN 77
+G G + + T L V +LDF V+D+ + +LF++ G + V D S RSLG V+
Sbjct: 24 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG-RSLGTADVH 82
Query: 78 YANPADAARALDVLNFTPLNNKSIRI 103
+ ADA +A+ PL+ + + I
Sbjct: 83 FERRADALKAMKQYKGVPLDGRPMDI 108
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+ + NLD + + + F+ FG + + D SG+S G V FE + A A+ +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 180 GMLIN 184
G+ ++
Sbjct: 98 GVPLD 102
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 179 N 179
N
Sbjct: 68 N 68
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 38/72 (52%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LYVG L V D L+ F G + +++ D T + G+ +V + DAA A+D +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 92 NFTPLNNKSIRI 103
N + L ++IR+
Sbjct: 68 NESELFGRTIRV 79
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 373 NGKMIVSKPLYVAVAQ 388
N + + + V +A+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 36.2 bits (82), Expect = 0.059, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 269
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 270 NGKKFDDREWYVGKAQ 285
N + R V A+
Sbjct: 68 NESELFGRTIRVNLAK 83
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 30/85 (35%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 369
G ++I L E L+E F +FG + C VMRDP + S+G GFV F + L
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 370 A----EMNGKMIVSKPLYVAVAQRK 390
A E++ K I K + AQ K
Sbjct: 85 AQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 15 PNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYG 74
P G G+SG +++G L + T L + F Q G+V V RD T+RS G+G
Sbjct: 16 PRGSHMGSSG-----CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70
Query: 75 YVNYANPADAARAL 88
+V + + A + L
Sbjct: 71 FVTFMDQAGVDKVL 84
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDA----AKA 265
+F+ L TT E L++ FG++G + +VMRD +S+ FGFV F + A++
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 266 VEALNGKKFDDREWYVGKAQKK 287
L+ K D + + +AQ K
Sbjct: 88 RHELDSKTIDPKVAFPRRAQPK 109
Score = 33.1 bits (74), Expect = 0.43, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+FI L + L + F FG + C + D + +S+GFGFV F + Q +DK+
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD----QAGVDKV 83
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 39/163 (23%), Positives = 77/163 (47%), Gaps = 16/163 (9%)
Query: 31 SLYVGDLDFNVTDSQLY----DLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
+L+VG+L+FN + +L D+F++ L+V R TR+ +GYV++ + D +
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAK--NDLAVVDVRIGMTRK---FGYVDFESAEDLEK 63
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI-L 145
AL++ N+ I++ S ++ + KNL + L + F I L
Sbjct: 64 ALELTGLKVFGNE-IKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRL 122
Query: 146 SCKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQV 188
K G+SKG +++F+ + A+ ++ G I+ + +
Sbjct: 123 VSK-----DGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 46/169 (27%), Positives = 77/169 (45%), Gaps = 23/169 (13%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
N+FV NL+ + + +LK + V+ G ++ FG+V+FE+A+D KA+E L
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE-L 67
Query: 270 NGKKFDDREWYVGKAQ-KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 328
G K E + K + K S++E++ + L KNL + ++L
Sbjct: 68 TGLKVFGNEIKLEKPKGKDSKKERDAR-----------------TLLAKNLPYKVTQDEL 110
Query: 329 KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI 377
KE+F + I + G SKG ++ F T +A + E G I
Sbjct: 111 KEVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
>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 = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
+++ L + +D K LH F FG+I +I D + + +GF FV+FE E A AID +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 179 N 179
N
Sbjct: 70 N 70
Score = 43.1 bits (100), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 38/72 (52%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LYVG L V D L+ F G + +++ D T + G+ +V + DAA A+D +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 92 NFTPLNNKSIRI 103
N + L ++IR+
Sbjct: 70 NESELFGRTIRV 81
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 373 NGKMIVSKPLYVAVAQ 388
N + + + V +A+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 35.8 bits (81), Expect = 0.065, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 269
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 270 NGKKFDDREWYVGKAQ 285
N + R V A+
Sbjct: 70 NESELFGRTIRVNLAK 85
>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 = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDK 177
++F+ +L I A+ F+ FG I ++ D +G+SKG+GFV F NK A+NAI +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 178 LNGMLINDKQVFVGHFLRK 196
+ G + +Q+ RK
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 3/90 (3%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
G G+ F ++VGDL +T + + F+ G++ RV +D++T +S GYG+V++ N
Sbjct: 1 GPLGSHF---HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 57
Query: 81 PADAARALDVLNFTPLNNKSIRIMYSHRDP 110
DA A+ + L + IR ++ R P
Sbjct: 58 KWDAENAIQQMGGQWLGGRQIRTNWATRKP 87
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 268
+VFV +L T + F +G I+ A V++D GKSK +GFV+F N DA A++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 269 LNGKKFDDREWYVGKAQKK 287
+ G+ R+ A +K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 37.4 bits (85), Expect = 0.023, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 335 FGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 390
FG I+ +V++D +G SKG GFV+F +A A+ +M G+ + + + A RK
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
V+V NL + +L++ FG YG + S V R+ G F FV FE+ DAA AV L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 271 GK 272
G+
Sbjct: 132 GR 133
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
+Y+ NLG++ + +L+ F +G + S V R+P G + FV F P +A+ A+ E++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRELD 131
Query: 374 GKMI 377
G+ +
Sbjct: 132 GRTL 135
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
L +YVG+L N ++L F G + SV V R+ G+ +V + +P DAA A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADA 126
Query: 88 LDVLNFTPLNNKSIRIMYSH 107
+ L+ L +R+ S+
Sbjct: 127 VRELDGRTLCGCRVRVELSN 146
Score = 32.3 bits (72), Expect = 0.69, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+++ NL + + L F +G + S +A + GF FV+FE+ A +A+ +L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELD 131
Query: 180 G 180
G
Sbjct: 132 G 132
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
TSL V +L + + L +F + G+V V + RD T+ S G+ +V + + DA A+D
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 90 VLNFTPLNNKSIRI 103
++ L+ + +R+
Sbjct: 131 AMDGAVLDGRELRV 144
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 271
V NL T+ + L+++F +YG + + RD K S+ F FV F + DA A++A++G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 272 KKFDDREWYVGKAQ 285
D RE V A+
Sbjct: 135 AVLDGRELRVQMAR 148
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 116 GTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNA 174
G ++ + NL L F +G + I D + +S+GF FV+F +K A++A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 175 IDKLNGMLINDKQVFV 190
+D ++G +++ +++ V
Sbjct: 129 MDAMDGAVLDGRELRV 144
Score = 33.9 bits (76), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 371
+L + NL + L+ +F ++G + + RD + S+G FV F +A A+
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 372 MNGKMIVSKPLYVAVAQ 388
M+G ++ + L V +A+
Sbjct: 132 MDGAVLDGRELRVQMAR 148
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+Y+G + ++ T+ Q+ DL S VG V+++++ D T RS GY ++ + + +A A+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 92 NFTPLNNKSIRIMYS 106
N L ++ ++ YS
Sbjct: 67 NGYQLGSRFLKCGYS 81
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+++ ++ + + D S+ G +++ K+ D +G+SKG+ F++F + ES+ +A+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 179 NGMLINDKQVFVGH 192
NG + + + G+
Sbjct: 67 NGYQLGSRFLKCGY 80
Score = 36.6 bits (83), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 372
+Y+ ++ +E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 373 NGKMIVSK 380
NG + S+
Sbjct: 67 NGYQLGSR 74
Score = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 270 NGKKFDDR 277
NG + R
Sbjct: 67 NGYQLGSR 74
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+Y+G + ++ T+ Q+ DL S VG V+++++ D T RS GY ++ + + +A A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 92 NFTPLNNKSIRIMYS 106
N L ++ ++ YS
Sbjct: 65 NGYQLGSRFLKCGYS 79
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+++ ++ + + D S+ G +++ K+ D +G+SKG+ F++F + ES+ +A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 179 NGMLINDKQVFVGH 192
NG + + + G+
Sbjct: 65 NGYQLGSRFLKCGY 78
Score = 35.8 bits (81), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 325 DEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL 382
+E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +NG + S+ L
Sbjct: 16 EEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 74
Score = 33.9 bits (76), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 270 NGKKFDDR 277
NG + R
Sbjct: 65 NGYQLGSR 72
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
V+V NL + +L++ FG YG + S V R+ G F FV FE+ DAA AV L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 271 GK 272
G+
Sbjct: 132 GR 133
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
+Y+ NLG++ + +L+ F +G + S V R+P G + FV F P +A+ A+ +++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRDLD 131
Query: 374 GKMI 377
G+ +
Sbjct: 132 GRTL 135
Score = 33.5 bits (75), Expect = 0.34, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARA 87
L +YVG+L N ++L F G + SV V R+ G+ +V + +P DAA A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADA 126
Query: 88 LDVLNFTPLNNKSIRIMYSH 107
+ L+ L +R+ S+
Sbjct: 127 VRDLDGRTLCGCRVRVELSN 146
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+++ NL + + L F +G + S +A + GF FV+FE+ A +A+ L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRDLD 131
Query: 180 G 180
G
Sbjct: 132 G 132
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 264
T F +FV L TTD L+K F +G I AVV+ D GKS+ +GFV + A +
Sbjct: 15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74
Query: 265 AVE----ALNGKKFDDREWYVG 282
A + ++G+K + Y+G
Sbjct: 75 ACKDPNPIIDGRKANVNLAYLG 96
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 31/59 (52%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
T ++VG L ++ TD+ L F G + V D T +S GYG+V A+ A A RA
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Score = 36.2 bits (82), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
IF+ L +L F FG+I + TD +G+S+G+GFV ++ +A+ A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 179 NGML 182
N ++
Sbjct: 80 NPII 83
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
+++ L D L++ F FG I V+ D +G S+G GFV + A RA +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 373 N 373
N
Sbjct: 80 N 80
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
+Y+G + ++ T+ Q+ DL S VG V+++++ D T RS GY ++ + + +A A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 92 NFTPLNNKSIRIMYS 106
N L ++ ++ YS
Sbjct: 66 NGYQLGSRFLKCGYS 80
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+++ ++ + + D S+ G +++ K+ D +G+SKG+ F++F + ES+ +A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 179 NGMLINDKQVFVGH 192
NG + + + G+
Sbjct: 66 NGYQLGSRFLKCGY 79
Score = 36.2 bits (82), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 325 DEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL 382
+E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +NG + S+ L
Sbjct: 17 EEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 75
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 269
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 270 NGKKFDDR 277
NG + R
Sbjct: 66 NGYQLGSR 73
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+FV+ + +L +IFG +G + ++ F FV FE A+ AAKA+E ++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEEVH 86
Query: 271 GKKFDDREWYVGKAQKKSER 290
GK F ++ V ++ ++R
Sbjct: 87 GKSFANQPLEVVYSKLPAKR 106
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L+++ + + +L E+F FG + K++ G FV F E A++A+ E++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVH 86
Query: 374 GKMIVSKPLYVAVAQRKEER 393
GK ++PL V ++ +R
Sbjct: 87 GKSFANQPLEVVYSKLPAKR 106
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F++ + L++ F FG + KI GF FV+FE ESA AI++++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 86
Query: 180 G 180
G
Sbjct: 87 G 87
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L Y +FSQ GQ+L + V R L R G +V + + A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 370 AEMNGKMIVSKPLYVAVAQ 388
M G KP+ + A+
Sbjct: 70 RSMQGFPFYDKPMRIQYAK 88
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF ++G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
A+ ++ G F D+ + A+ S+
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSD 92
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LY+ +L + +T ++YD+F + G + +RV TR G YV Y + DA A D L
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 77
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSGT 117
+ + N+ + ++Y + + + +K T
Sbjct: 78 SGFNVCNRYLVVLYYNANRAFQKMDT 103
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 28/117 (23%), Positives = 56/117 (47%), Gaps = 16/117 (13%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
++I+NL I + ++D F +G I ++ + +++G +V +E+ A+NA D L+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT 236
G + ++ + V ++ N F K +D +E LK + +YG T
Sbjct: 79 GFNVCNRYLVVLYY-------------NANRAFQK-MDTKKKEEQLKLLKEKYGINT 121
Score = 34.3 bits (77), Expect = 0.21, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 78
Query: 374 GKMIVSKPLYV 384
G + ++ L V
Sbjct: 79 GFNVCNRYLVV 89
Score = 33.1 bits (74), Expect = 0.47, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 44/80 (55%), Gaps = 5/80 (6%)
Query: 194 LRKQERETVAIKTKFNNV-FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCF 251
++ +R + + + N + +++NL T E++ IFG+YG I +R G+ +++
Sbjct: 3 MQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGT 59
Query: 252 GFVNFENADDAAKAVEALNG 271
+V +E+ DA A + L+G
Sbjct: 60 AYVVYEDIFDAKNACDHLSG 79
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 372
L+I L + ++D+++KEL + FG + + +++D +G+SKG F + +A+A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 373 NGKMIVSKPLYV 384
NG + K L V
Sbjct: 64 NGMQLGDKKLLV 75
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKL 178
+FI L ++ + + +SFG + + + D +G SKG+ F ++ + AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 179 NGMLINDKQVFV 190
NGM + DK++ V
Sbjct: 64 NGMQLGDKKLLV 75
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L++G L + D Q+ +L + G + + + +D +T S GY + Y + +A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 92 NFTPLNNKSIRI 103
N L +K + +
Sbjct: 64 NGMQLGDKKLLV 75
>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 = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 46/168 (27%), Positives = 77/168 (45%), Gaps = 21/168 (12%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
N+F+ NL+ + + +LK E V+ G ++ FG+V+FE+A+D KA+E L
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 270 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 329
G K E + K KG+ + ++ L KNL +I +++LK
Sbjct: 74 TGLKVFGNEIKLEKP----------KGRDSKKVR------AARTLLAKNLSFNITEDELK 117
Query: 330 ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI 377
E+F + I + G SKG ++ F + +A + L E G I
Sbjct: 118 EVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/158 (21%), Positives = 78/158 (49%), Gaps = 6/158 (3%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
+L++G+L+ N + ++L S++ + V D+ T + +GYV++ + D +AL++
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALEL 73
Query: 91 LNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIA 150
N+ I++ S + + KNL +I L + F + L ++
Sbjct: 74 TGLKVFGNE-IKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFE---DALEIRLV 129
Query: 151 TDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQV 188
+ G+SKG +++F+++ A+ +++ G I+ + V
Sbjct: 130 SQ-DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LY+ +L + +T ++YD+F + G + +RV TR G YV Y + DA A D L
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 71
Query: 92 NFTPLNNKSIRIMY 105
+ + N+ + ++Y
Sbjct: 72 SGFNVCNRYLVVLY 85
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
++I+NL I + ++D F +G I ++ + +++G +V +E+ A+NA D L+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 72
Query: 180 GMLINDKQVFVGHF 193
G + ++ + V ++
Sbjct: 73 GFNVCNRYLVVLYY 86
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 72
Query: 374 GKMIVSKPLYV 384
G + ++ L V
Sbjct: 73 GFNVCNRYLVV 83
Score = 33.1 bits (74), Expect = 0.42, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 199 RETVAIKTKFNNV-FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNF 256
R + + + N + +++NL T E++ IFG+YG I +R G+ +++ +V +
Sbjct: 2 RANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVY 58
Query: 257 ENADDAAKAVEALNG 271
E+ DA A + L+G
Sbjct: 59 EDIFDAKNACDHLSG 73
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEALNG 271
V NL T+ + L+++F +YG + + R+ K+ + F FV F + DA A A++G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 272 KKFDDREWYV 281
+ D RE V
Sbjct: 78 AELDGRELRV 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: 204 IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 263
+ K +FV+NL + T+E L+K F E+G + ++D + FV+FE+ A
Sbjct: 11 VMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAV 63
Query: 264 KAVEALNGK 272
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: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L+++NL ++ +E L++ FSEFG + K ++D FV F A +A+ EMN
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 374 GKMIVSKPLYVAVAQRKEERRA 395
GK I + + + +A+ +++R+
Sbjct: 71 GKEIEGEEIEIVLAKPPDKKRS 92
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F++NL ++ + L +FS FG + K D + FV FE++ +A A+D++N
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 180 G 180
G
Sbjct: 71 G 71
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 19 AAGASGNQFLTTS---LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
++G+SG+ + L+V +L VT+ L FS+ G++ V+ +D Y +
Sbjct: 2 SSGSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAF 53
Query: 76 VNYANPADAARALDVLN 92
V++ + A +A+D +N
Sbjct: 54 VHFEDRGAAVKAMDEMN 70
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ V N+ + T+++L+ F EYG + +++D + FV+ E A+DA +A+ L+
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 271 GKKFDDREWYV 281
+F + +V
Sbjct: 66 NTEFQGKRMHV 76
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/77 (19%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L++ N+ + +++L+ F E+G + C +++D FV E+A A+ ++
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 374 GKMIVSKPLYVAVAQRK 390
K ++V ++ +
Sbjct: 66 NTEFQGKRMHVQLSTSR 82
>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 = 6e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 6/93 (6%)
Query: 313 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 368
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 401
L M G KP+ + A+ + A+++ F
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
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: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 3 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 58
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ + G DK
Sbjct: 59 KEVSSATNALRSMQGFPFYDK 79
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 46/94 (48%), Gaps = 6/94 (6%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 298
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>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: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAV 266
F +FV ++ TT+ L++ F YG I +V GK + + F+ +E+ D A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 267 EALNGKKFDDR 277
+ +GKK D R
Sbjct: 162 KHADGKKIDGR 172
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 101 IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCK-IATDGSGQSKG 159
+++ H DP+ + +F+ ++ L F +G I + + SG+ +G
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 160 FGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
+ F+++E++ +A +G I+ ++V V
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
Score = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 3 QIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVC 62
Q +V+ + +M P+ A G+ F T L+V ++++ T+S+L F G + + +
Sbjct: 79 QQEVETELKMWDPHN-DPNAQGDAFKT--LFVARVNYDTTESKLRREFEVYGPIKRIHMV 135
Query: 63 RDLSTRRSLGYGYVNYANPADAARA 87
+ + GY ++ Y + D A
Sbjct: 136 YSKRSGKPRGYAFIEYEHERDMHSA 160
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD--GSGQSKGFGFVQFENKES 170
+K T I ++N+ + + + + FS+FG + + ++ G+G +GFGFV F K+
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 171 AQNAIDKL 178
A+ A + L
Sbjct: 71 AKKAFNAL 78
Score = 36.2 bits (82), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 202 VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENA 259
V K + + V+N+ +++++F +G + + + + G G + FGFV+F
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 260 DDAAKAVEAL 269
DA KA AL
Sbjct: 69 QDAKKAFNAL 78
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS--KGSGFVAFSTPEEASRAL 369
+ ++N+ + +++ELFS FG + + ++ + +G +G GFV F T ++A +A
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
>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 = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 39/72 (54%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+FI L S + L + + G + ++ T+ +G+ KG +V++EN+ A A+ K++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 180 GMLINDKQVFVG 191
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: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L+I L S E+L+E+ GT+ +++ + +G KG +V + +AS+A+ +M+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 374 GKMIVSKPLYVAVA 387
G I + VA++
Sbjct: 80 GMTIKENIIKVAIS 93
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 36/63 (57%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
+ +F+ L S T E+L++I +GT+ ++ + GK K +V +EN A++AV
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77
Query: 269 LNG 271
++G
Sbjct: 78 MDG 80
Score = 32.3 bits (72), Expect = 0.87, Method: Composition-based stats.
Identities = 24/98 (24%), Positives = 49/98 (50%), Gaps = 6/98 (6%)
Query: 19 AAGASGNQFLTTSL-----YVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGY 73
++G+SG +TSL ++ L F+ T +L ++ G V +R+ + + + G
Sbjct: 2 SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPK-GL 60
Query: 74 GYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPS 111
YV Y N + A++A+ ++ + I++ S+ PS
Sbjct: 61 AYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS 98
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+FV+ + +L +IFG +G + ++ F FV FE A+ AAKA+E ++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEEVH 59
Query: 271 GKKFDDR 277
GK F ++
Sbjct: 60 GKSFANQ 66
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L+++ + + +L E+F FG + K++ G FV F E A++A+ E++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 374 GKMIVSKPLYVAVAQ 388
GK ++PL V ++
Sbjct: 60 GKSFANQPLEVVYSK 74
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F++ + L++ F FG + KI GF FV+FE ESA AI++++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 180 G 180
G
Sbjct: 60 G 60
>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 = 9e-04, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 370
++I L E L+E F +FG + C VMRDP + S+G GFV F + LA
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 371 --EMNGKMIVSK 380
E++ K I K
Sbjct: 63 RHELDSKTIDPK 74
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
+++G L + T L + F Q G+V V RD T+RS G+G+V + + A + L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNF 256
+F+ L TT E L++ FG++G + +VMRD +S+ FGFV F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 33.5 bits (75), Expect = 0.36, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+FI L + L + F FG + C + D + +S+GFGFV F + Q +DK+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD----QAGVDKV 58
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/96 (29%), Positives = 46/96 (47%), Gaps = 10/96 (10%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
G+SG+ T ++VG++ T +L LF + G+V+ V +D Y +V+
Sbjct: 1 GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEK 52
Query: 81 PADAARALDVLNFTPLNNKSIRIMYSHRDPSIRKSG 116
ADA A+ LN + K I + S + +KSG
Sbjct: 53 EADAKAAIAQLNGKEVKGKRINVELSTKGQ--KKSG 86
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+FV N+ + T ++L+ +F G + V++D + FV+ E DA A+ LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 271 GKKFDDREWYV---GKAQKKS 288
GK+ + V K QKKS
Sbjct: 65 GKEVKGKRINVELSTKGQKKS 85
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
T IF+ N+ + + L F G ++ C + D + FV E + A+ AI
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIA 61
Query: 177 KLNGMLINDKQVFV 190
+LNG + K++ V
Sbjct: 62 QLNGKEVKGKRINV 75
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 267
+FV L +TT ED+K F ++G + A++M D + + FGFV FE+ D K E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
Score = 35.8 bits (81), Expect = 0.063, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
++VG L N T + F Q G+V + D +T R G+G+V + + D + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60
Query: 92 NFTPLNNKSI 101
+F +NNK +
Sbjct: 61 HFHEINNKMV 70
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 26/100 (26%), Positives = 47/100 (47%), Gaps = 13/100 (13%)
Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
+ +Y+ NLG +L+ FS +G + + + R+P G + FV F P +A A+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFA----FVEFEDPRDAEDAVRG 56
Query: 372 MNGKMIVSKPLYVAVA---------QRKEERRARLQAQFS 402
++GK+I + V ++ R RR L+ F+
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFN 96
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
V+V NL +L++ F YG + + + R+ G F FV FE+ DA AV L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 58
Query: 271 GK 272
GK
Sbjct: 59 GK 60
Score = 35.4 bits (80), Expect = 0.097, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+++ NL L FS +G + + IA + GF FV+FE+ A++A+ L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLD 58
Query: 180 GMLINDKQVFV 190
G +I +V V
Sbjct: 59 GKVICGSRVRV 69
>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: 509 EQQRTLLGESLYPLV--EQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEV 566
++QR LGE LY V + +AA K+TGM+L++ EV LLES E + EA
Sbjct: 18 QKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAA 77
Query: 567 LRSVAQQQ 574
S ++Q
Sbjct: 78 YESFKKEQ 85
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 4 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 59
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ + G DK
Sbjct: 60 KEVSSATNALRSMQGFPFYDK 80
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDI 93
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: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 398
M G KP+ + A+ + A+++
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 36.2 bits (82), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELK 295
A+ ++ G F D+ + A+ S+ ++K
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
>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: 208 FNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAV 266
F +FV ++ TT+ L++ F YG I +V GK + + F+ +E+ D A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 267 EALNGKKFDDR 277
+ +GKK D R
Sbjct: 162 KHADGKKIDGR 172
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 101 IRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCK-IATDGSGQSKG 159
+++ H DP+ + +F+ ++ L F +G I + + SG+ +G
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 160 FGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
+ F+++E++ +A +G I+ ++V V
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 3 QIQVQHQAQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVC 62
Q +V+ + +M P+ A G+ F T L+V ++++ T+S+L F G + + +
Sbjct: 79 QQEVETELKMWDPHN-DPNAQGDAFKT--LFVARVNYDTTESKLRREFEVYGPIKRIHMV 135
Query: 63 RDLSTRRSLGYGYVNYANPAD 83
+ + GY ++ Y + D
Sbjct: 136 YSKRSGKPRGYAFIEYEHERD 156
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 3 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 58
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ + G DK
Sbjct: 59 KEVSSATNALRSMQGFPFYDK 79
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDI 92
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: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 370 AEMNGKMIVSKPLYVAVAQ 388
M G KP+ + A+
Sbjct: 69 RSMQGFPFYDKPMRIQYAK 87
Score = 36.2 bits (82), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
A+ ++ G F D+ + A+ S+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 3 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 58
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ + G DK
Sbjct: 59 KEVSSATNALRSMQGFPFYDK 79
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDI 92
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: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 398
M G KP+ + A+ + A+++
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 36.2 bits (82), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDI 93
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: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 4 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 59
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ + G DK
Sbjct: 60 KEVSSATNALRSMQGFPFYDK 80
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: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 398
M G KP+ + A+ + A+++
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 265 AVEALNGKKFDDREWYVGKAQKKSEREQELKG 296
A+ ++ G F D+ + A+ S+ ++KG
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKG 99
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 63
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAKTDSDI 89
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: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 65
Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 398
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: 120 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
I+I NL++ I K+LH FS FG IL I S + +G FV F+ SA NA+
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNAL 65
Query: 176 DKLNGMLINDK 186
+ G DK
Sbjct: 66 RSMQGFPFYDK 76
Score = 35.8 bits (81), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 6 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 63
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
A+ ++ G F D+ + A+ S+
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAKTDSD 88
>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 = 30/81 (37%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 1 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIF 56
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ + G DK
Sbjct: 57 KEVSSATNALRSMQGFPFYDK 77
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 64
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAKTDSDI 90
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: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 66
Query: 370 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 398
M G KP+ + A+ + A+++
Sbjct: 67 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 95
Score = 35.8 bits (81), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 64
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
A+ ++ G F D+ + A+ S+
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAKTDSD 89
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L + +L + +T ++YD+F + G + +RV TR G YV Y + DA A D L
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 77
Query: 92 NFTPLNNKSIRIMYSHRDPSIRKSGT 117
+ + N+ + ++Y + + + +K T
Sbjct: 78 SGFNVCNRYLVVLYYNANRAFQKMDT 103
Score = 37.7 bits (86), Expect = 0.020, Method: Composition-based stats.
Identities = 28/117 (23%), Positives = 55/117 (47%), Gaps = 16/117 (13%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+ I+NL I + ++D F +G I ++ + +++G +V +E+ A+NA D L+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT 236
G + ++ + V ++ N F K +D +E LK + +YG T
Sbjct: 79 GFNVCNRYLVVLYY-------------NANRAFQK-MDTKKKEEQLKLLKEKYGINT 121
Score = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 194 LRKQERETVAIKTKFNNVF-VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCF 251
++ +R + + + N + ++NL T E++ IFG+YG I +R G+ +++
Sbjct: 3 MQAAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGT 59
Query: 252 GFVNFENADDAAKAVEALNG 271
+V +E+ DA A + L+G
Sbjct: 60 AYVVYEDIFDAKNACDHLSG 79
>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: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
+ L+I + ++D++ LK LF EFG I V++D +G+ KG F+ + E A +A +
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Query: 371 EMN 373
++
Sbjct: 74 ALH 76
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
+FI + +++D K L F FG I + D +G KG F+ + +ESA A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 178 LN 179
L+
Sbjct: 75 LH 76
Score = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
+F+ + + ++DLK +F E+G I V++D G K F+ + + A KA A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 269 LNGKK 273
L+ +K
Sbjct: 75 LHEQK 79
>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: 297 QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGF 356
+FE + ++ K +Y + + D+ +++ FS FG I +V + KG F
Sbjct: 13 RFEDVVNQSSPK--NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSF 65
Query: 357 VAFSTPEEASRALAEMNGKMI 377
V FST E A+ A+ +NG I
Sbjct: 66 VRFSTHESAAHAIVSVNGTTI 86
Score = 37.4 bits (85), Expect = 0.026, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
++ + + + + TFS FG I+ ++ + KG+ FV+F ESA +AI +N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 180 GMLI 183
G I
Sbjct: 83 GTTI 86
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
++Y G + +TD + FS GQ++ +RV + GY +V ++ AA A+
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80
Query: 91 LNFTPLNNKSIRIMYSHRDPSI 112
+N T + ++ + P +
Sbjct: 81 VNGTTIEGHVVKCYWGKESPDM 102
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 12/75 (16%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
SG +FI NL + + + F +G +L C I K +GFV E+K +A++A
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58
Query: 175 ID-----KLNGMLIN 184
I KL+G+ IN
Sbjct: 59 IRNLHHYKLHGVNIN 73
Score = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 9/86 (10%)
Query: 21 GASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYAN 80
G+SG+ + L++G+L T+ ++ LF Q G+VL + ++ YG+V+ +
Sbjct: 1 GSSGSSGMV-KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIED 51
Query: 81 PADAARALDVLNFTPLNNKSIRIMYS 106
A A+ L+ L+ +I + S
Sbjct: 52 KTAAEDAIRNLHHYKLHGVNINVEAS 77
>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: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 63
Query: 370 AEMNGKMIVSKPLYVAVAQ 388
M G KP+ + A+
Sbjct: 64 RSMQGFPFYDKPMRIQYAK 82
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 61
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTDSDI 87
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: 120 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
I+I NL++ I K+LH FS FG IL I S + +G FV F+ SA NA+
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNAL 63
Query: 176 DKLNGMLINDK 186
+ G DK
Sbjct: 64 RSMQGFPFYDK 74
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: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 61
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
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: 314 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 64
Query: 370 AEMNGKMIVSKPLYVAVAQ 388
M G KP+ + A+
Sbjct: 65 RSMQGFPFYDKPMRIQYAK 83
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 62
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL + P +K +RI Y+ D I
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKTDSDI 88
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: 120 IFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
I+I NL++ I K+LH FS FG IL I S + +G FV F+ SA NA+
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNAL 64
Query: 176 DKLNGMLINDK 186
+ G DK
Sbjct: 65 RSMQGFPFYDK 75
Score = 35.8 bits (81), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 5 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 62
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
A+ ++ G F D+ + A+ S+
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKTDSD 87
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTIT--SAVVMRDGDGKSKCFGFVNFENADDAAK 264
K V + L + T + + +IF YG I V R SK + +V FEN D+A K
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 265 AVEALNGKKFDDRE 278
A++ ++G + D +E
Sbjct: 63 ALKHMDGGQIDGQE 76
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTIT--SCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
++I L ++ + + E+FS +G I V R +SKG +V F P+EA +AL
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 372 MNGKMI 377
M+G I
Sbjct: 67 MDGGQI 72
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR-----SLGYGYVNYANPADA 84
T +++G L NVT + ++FS G++ + D+ R S GY YV + NP +A
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMI----DMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 85 ARALDVLNFTPLNNKSI 101
+AL ++ ++ + I
Sbjct: 61 EKALKHMDGGQIDGQEI 77
Score = 35.8 bits (81), Expect = 0.077, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNI--LSCKIATDGSGQSKGFGFVQFENKESAQNAIDK 177
+ I L +++ + + FS++G I + + SKG+ +V+FEN + A+ A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 178 LNGMLINDKQV 188
++G I+ +++
Sbjct: 67 MDGGQIDGQEI 77
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 5/65 (7%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
++V+NL ST++E ++K E+ I V R K + + FV+F N +DA +A++ALN
Sbjct: 18 LYVRNLMLSTSEEMIEK---EFNNIKPGAVERVK--KIRDYAFVHFSNREDAVEAMKALN 72
Query: 271 GKKFD 275
GK D
Sbjct: 73 GKVLD 77
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 314 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 371
LY++NL S +E +++ F+ G + K +RD FV FS E+A A+
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-------YAFVHFSNREDAVEAMKA 70
Query: 372 MNGKMIVSKPLYVAVAQ 388
+NGK++ P+ V +A+
Sbjct: 71 LNGKVLDGSPIEVTLAK 87
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 46 LYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMY 105
LY +FSQ GQ+L + + L R G +V + A+ AL + P +K ++I Y
Sbjct: 27 LYAIFSQFGQILDIVALKTLKMR---GQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAY 83
Query: 106 SHRDPSI 112
S D I
Sbjct: 84 SKSDSDI 90
Score = 35.4 bits (80), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 7/98 (7%)
Query: 313 NLYIKNLGDSIDDE----KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 368
+YI NL + I E L +FS+FG I ++ +G FV F AS A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVIFKEIGSASNA 65
Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 406
L M G KP+ +A ++ + A+++ F + RP
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKE-RP 102
Score = 32.3 bits (72), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 22/99 (22%), Positives = 47/99 (47%), Gaps = 6/99 (6%)
Query: 210 NVFVKNLDEST----TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 265
+++ NL+E + L IF ++G I V ++ + + FV F+ A+ A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQA--FVIFKEIGSASNA 65
Query: 266 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 304
+ + G F D+ + ++ S+ ++KG F++ K+
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKERPKK 104
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 28 LTTSLYVGDLDFNVTDSQLYDLFSQVGQ-VLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
+ SL++GDL+ + ++ + F+ +G+ V+SV++ R+ T GY +V +A+ A A +
Sbjct: 8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67
Query: 87 ALDVLNFTPL 96
L +N PL
Sbjct: 68 CLHKINGKPL 77
Score = 33.5 bits (75), Expect = 0.33, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
+L++ +L +D+ + F+ G T+ S K++R+ +GI G FV F+ A + L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 371 EMNGK 375
++NGK
Sbjct: 71 KINGK 75
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 118 GNIFIKNLDKSIDHKALHDTFSSFG-NILSCKIATDG-SGQSKGFGFVQFENKESAQNAI 175
++++ +L+ +D + F++ G ++S KI + +G G+ FV+F + +A+ +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 176 DKLNG 180
K+NG
Sbjct: 70 HKING 74
>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 = 0.009, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 312 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 370
+ L++ + +D++ LK LF EFG I V++D +G+ KG F+ + + A +A +
Sbjct: 16 IKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQS 75
Query: 371 EMN 373
++
Sbjct: 76 ALH 78
Score = 35.4 bits (80), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 268
+FV + ++DLK +F E+G I V++D G K F+ + D A KA A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 269 LNGKK 273
L+ +K
Sbjct: 77 LHEQK 81
Score = 29.6 bits (65), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
+F+ + + +D + L F FG I + D +G KG F+ + ++SA A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 178 LN 179
L+
Sbjct: 77 LH 78
>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 = 38.9 bits (89), Expect = 0.009, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 110 PSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFEN 167
P ++S G I F+ + + + +HD F+ +G I + + D +G KG+ V++E
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 168 KESAQNAIDKLNG 180
+ AQ A++ LNG
Sbjct: 61 YKEAQAAMEGLNG 73
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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 270 NGK 272
NG+
Sbjct: 72 NGQ 74
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 35/72 (48%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+V + T+ ++D F++ G++ ++ + D T GY V Y +A A++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 92 NFTPLNNKSIRI 103
N L + I +
Sbjct: 72 NGQDLMGQPISV 83
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 7/84 (8%)
Query: 314 LYIKNLGDSIDDEKLKELFSEF----GTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
LY+KNL + + L LF+ F G ++M +G +G F+ F E A +AL
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQAL 84
Query: 370 AEMNGKMIVSKPLYVAVAQRKEER 393
+NG + K L + + K++R
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQR 108
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 120 IFIKNLDKSIDHKALHDTFSSF----GNILSCKIATDGSGQSKGFGFVQFENKESAQNAI 175
+++KNL + + L F+ F G + ++ T G+ +G F+ F NKE A A+
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT---GRMRGQAFITFPNKEIAWQAL 84
Query: 176 DKLNGMLINDKQVFVGHFLRKQERET 201
+NG + K + + K++R +
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSS 110
Score = 33.1 bits (74), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVV-MRDGDGKSKCFGFVNFENADDAAKAVEAL 269
+++KNL T+ DL +F + + R G+ + F+ F N + A +A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 270 NGKKFDDREWYVGKAQKKSER 290
NG K + + + K +R
Sbjct: 88 NGYKLYGKILVIEFGKNKKQR 108
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
LY+ +L VT+ L LF++ + + + T R G ++ + N A +AL ++
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 92 NFTPLNNKSIRIMY 105
N L K + I +
Sbjct: 88 NGYKLYGKILVIEF 101
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 30/81 (37%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 3 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIF 58
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ G DK
Sbjct: 59 KEVSSATNALRSXQGFPFYDK 79
Score = 37.4 bits (85), Expect = 0.022, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIFKEVSSATN 66
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL P +K RI Y+ D I
Sbjct: 67 ALRSXQGFPFYDKPXRIQYAKTDSDI 92
Score = 33.1 bits (74), Expect = 0.50, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 66
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
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 = 0.010, Method: Composition-based stats.
Identities = 30/81 (37%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 4 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIF 59
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ G DK
Sbjct: 60 KEVSSATNALRSXQGFPFYDK 80
Score = 37.4 bits (85), Expect = 0.022, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIFKEVSSATN 67
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL P +K RI Y+ D I
Sbjct: 68 ALRSXQGFPFYDKPXRIQYAKTDSDI 93
Score = 33.1 bits (74), Expect = 0.50, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 67
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
A+ + G F D+ + A+ S+
Sbjct: 68 ALRSXQGFPFYDKPXRIQYAKTDSD 92
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 30/81 (37%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 110 PSIRKSGTGNIFIKNLDKSIDH----KALHDTFSSFGNILSCKIATDGSGQSKGFGFVQF 165
P R + T I+I NL++ I K+LH FS FG IL I S + +G FV F
Sbjct: 1 PETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKXRGQAFVIF 56
Query: 166 ENKESAQNAIDKLNGMLINDK 186
+ SA NA+ G DK
Sbjct: 57 KEVSSATNALRSXQGFPFYDK 77
Score = 37.4 bits (85), Expect = 0.023, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +L+ + +L + +FS+ GQ+L + V R L R G +V + + A
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIFKEVSSATN 64
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL P +K RI Y+ D I
Sbjct: 65 ALRSXQGFPFYDKPXRIQYAKTDSDI 90
Score = 33.1 bits (74), Expect = 0.50, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 209 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 64
Query: 265 AVEALNGKKFDDREWYVGKAQKKSE 289
A+ + G F D+ + A+ S+
Sbjct: 65 ALRSXQGFPFYDKPXRIQYAKTDSD 89
>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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 270 NGK 272
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: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+F+ + + + +HD F+ +G I + + D +G KG+ V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 179 NG 180
NG
Sbjct: 70 NG 71
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 35/72 (48%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+V + T+ ++D F++ G++ ++ + D T GY V Y +A A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92 NFTPLNNKSIRI 103
N L + I +
Sbjct: 70 NGQDLMGQPISV 81
>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 = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 270 NGK 272
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: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+F+ + + + +HD F+ +G I + + D +G KG+ V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 179 NG 180
NG
Sbjct: 70 NG 71
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 35/72 (48%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+V + T+ ++D F++ G++ ++ + D T GY V Y +A A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92 NFTPLNNKSIRI 103
N L + I +
Sbjct: 70 NGQDLMGQPISV 81
>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: 109 DPSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 166
+P ++S G I F+ + + + +HD F+ +G I + + D +G KG+ V++E
Sbjct: 14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 167 NKESAQNAIDKLNG 180
+ AQ A++ LNG
Sbjct: 74 TYKEAQAAMEGLNG 87
Score = 37.7 bits (86), Expect = 0.016, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 270 NGK 272
NG+
Sbjct: 86 NGQ 88
Score = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 35/72 (48%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+V + T+ ++D F++ G++ ++ + D T GY V Y +A A++ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 92 NFTPLNNKSIRI 103
N L + I +
Sbjct: 86 NGQDLMGQPISV 97
>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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 270 NGK 272
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: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDKL 178
+F+ + + + +HD F+ +G I + + D +G KG+ V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 179 NG 180
NG
Sbjct: 70 NG 71
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 35/72 (48%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+V + T+ ++D F++ G++ ++ + D T GY V Y +A A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92 NFTPLNNKSIRI 103
N L + I +
Sbjct: 70 NGQDLMGQPISV 81
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 120 IFIKNLDKSIDHKA-LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKL 178
+FI NL+ + K+ + FS +G I+ C + KGF FVQ+ N+ +A+ A+
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGE 70
Query: 179 NGMLI 183
+G +I
Sbjct: 71 DGRMI 75
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 365
D +G ++I+NL ++E L E+ +FG + +V+ P + SKG F F T E A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 366 SRALA 370
+ LA
Sbjct: 71 QKCLA 75
Score = 33.9 bits (76), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAI 175
+FI+NL + +AL + FG++ ++ + SKG F QF +E+AQ +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 7/91 (7%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAK 264
T+ VF++NL + +E L ++ ++G + VV+ SK F F + A K
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 265 AVEALN------GKKFDDREWYVGKAQKKSE 289
+ A + G K D R+ V A + E
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
>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 = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 109 DPSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 166
+P ++S G I F+ + + + +HD F+ +G I + + D +G KG+ V++E
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 167 NKESAQNAIDKLNG 180
+ AQ A++ LNG
Sbjct: 73 TYKEAQAAMEGLNG 86
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: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 269
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 270 NGK 272
NG+
Sbjct: 85 NGQ 87
Score = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 35/72 (48%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
L+V + T+ ++D F++ G++ ++ + D T GY V Y +A A++ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 92 NFTPLNNKSIRI 103
N L + I +
Sbjct: 85 NGQDLMGQPISV 96
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 13 SGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLG 72
SG +GV T+ L V L + T+ L + FS G+VL V+V +DL T S G
Sbjct: 3 SGSSGVKRAVQK----TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG 58
Query: 73 YGYVNY 78
+G+V +
Sbjct: 59 FGFVRF 64
Score = 37.4 bits (85), Expect = 0.023, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 117 TGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKES 170
T ++ + L + L + FS+FG +L ++ D +G SKGFGFV+F E+
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Score = 35.4 bits (80), Expect = 0.085, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 207 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKA 265
K +++ V L TT++DLK+ F +G + V +D G SK FGFV F + K
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 266 V 266
+
Sbjct: 74 M 74
Score = 34.7 bits (78), Expect = 0.17, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 325 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 371
++ LKE FS FG + +V +D +G SKG GFV F+ E + +++
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 364
++++ LG+++ E + + F + G I + K P +G KG V+F P
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 365 ASRALAEMNGKMIVSKPLYVAVAQRK 390
A A+ +GK P+ V+ A R+
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRR 95
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLS--------VRVCRDLSTRRSLGYGYVNYANPA 82
+++V L NVT + D F Q+G + + + + D T + G V++ +P
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 83 DAARALDVLNFTPLNNKSIRIMYSHR 108
A A+D + + I++ ++ R
Sbjct: 69 SAKAAIDWFDGKEFSGNPIKVSFATR 94
>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 = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 26/97 (26%), Positives = 44/97 (45%), Gaps = 5/97 (5%)
Query: 10 AQMSGPNGVAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR 69
A GP + + S+YVG++D+ T L FS G + + + D +
Sbjct: 17 AYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGH 76
Query: 70 SLGYGYVNYA--NPADAARALDVLNFTPLNNKSIRIM 104
GY Y+ +A N DAA A+D T ++I+++
Sbjct: 77 PKGYAYIEFAERNSVDAAVAMDE---TVFRGRTIKVL 110
Score = 32.3 bits (72), Expect = 0.79, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 8/84 (9%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
++++ N+D + L FSS G+I I D SG KG+ +++F + +N++D
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF----AERNSVDA 93
Query: 178 LNGMLINDKQVFVGHFLRKQERET 201
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: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNF--ENADDAAKAV 266
+V+V N+D +T +DL+ F G+I ++ D G K + ++ F N+ DAA A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 267 E 267
+
Sbjct: 98 D 98
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 40/68 (58%), Gaps = 7/68 (10%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAK 264
+ N +++ NL + T +DL+++FG+ + V+++ G + FV++ + + A +
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG------YAFVDYPDQNWAIR 59
Query: 265 AVEALNGK 272
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 = 0.018, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 270
+ + NL S T+E L+++F + I V ++ +GKSK + F+ F + +DA +A+ + N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 271 GKKFDDR 277
++ + R
Sbjct: 75 KREIEGR 81
Score = 35.8 bits (81), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L + NL S +E L+E+F + T KV ++ +G SKG F+ F++ E+A AL N
Sbjct: 18 LVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 374 GKMI 377
+ I
Sbjct: 75 KREI 78
Score = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+ + NL S + L + F I K+ + +G+SKG+ F++F + E A+ A++ N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 180 GMLINDKQV 188
I + +
Sbjct: 75 KREIEGRAI 83
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 29 TTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
+ +L + +L ++ T+ L ++F + ++V ++ +S GY ++ +A+ DA AL
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKA---TFIKVPQN-QNGKSKGYAFIEFASFEDAKEAL 70
Query: 89 DVLNFTPLNNKSIRI 103
+ N + ++IR+
Sbjct: 71 NSCNKREIEGRAIRL 85
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 11/76 (14%)
Query: 109 DPSIRKSGTGNIFIKNLDKSIDHKA-LHDTFSSFGNILSCKIATDGSGQSKGFGFVQFEN 167
DP KS +FI NL+ ++ K+ + FS +G + C + KG+ FVQ+ N
Sbjct: 22 DP---KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSN 71
Query: 168 KESAQNAIDKLNGMLI 183
+ A+ A+ NG ++
Sbjct: 72 ERHARAAVLGENGRVL 87
>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: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+ +KNL KS + ++ F G I+ +A D ++ F ++F + A AI K +
Sbjct: 7 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTH 65
Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV 239
++ ++ V H +++ N S T +++ + + + ++
Sbjct: 66 -KVVGQNEIIVSHLTE-------------CTLWMTNFPPSYTQRNIRDLLQDINVVALSI 111
Query: 240 VMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFD 275
+ S+ F +++ + +DA VE LNG K +
Sbjct: 112 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE 148
Score = 33.5 bits (75), Expect = 0.39, Method: Composition-based stats.
Identities = 31/155 (20%), Positives = 67/155 (43%), Gaps = 13/155 (8%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
T++ V +L + +++Y F G ++ V V L +++ + + +A A A+
Sbjct: 5 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KKNFRFARIEFARYDGALAAIT 62
Query: 90 VLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI-LSCK 148
+ N+ I+ SH +++ N S + + D + LS +
Sbjct: 63 KTHKVVGQNE---IIVSHLTEC-------TLWMTNFPPSYTQRNIRDLLQDINVVALSIR 112
Query: 149 IATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLI 183
+ + S+ F ++ +KE A+ ++KLNG+ I
Sbjct: 113 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI 147
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 36.6 bits (83), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYA 79
+++ L + L D FS VG+V VR+ D ++RRS G YV +
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 36.2 bits (82), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 11/70 (15%)
Query: 107 HRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFE 166
H P + GN+ +KN+ K + L FS +G+I+ I FGF+QF+
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSK----EDLFRIFSPYGHIMQINIKN-------AFGFIQFD 53
Query: 167 NKESAQNAID 176
N +S ++AI+
Sbjct: 54 NPQSVRDAIE 63
Score = 32.7 bits (73), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 64
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 36.2 bits (82), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 8/58 (13%)
Query: 120 IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
+FI NL K++ + L FS +G+I+ I FGF+QF+N +S ++AI+
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 75
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 36.2 bits (82), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 49/98 (50%), Gaps = 15/98 (15%)
Query: 191 GHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK- 249
G LRKQE + ++ N V K++D+ E + + G++G + ++ ++ G+ +
Sbjct: 7 GKLLRKQESTVMVLR---NMVDPKDIDDDLEGE-VTEECGKFGAVNRVIIYQEKQGEEED 62
Query: 250 ----CFGFVNFENADDAAKAVEALNGKKFDDREWYVGK 283
FV F A + KA++ALNG+ W+ G+
Sbjct: 63 AEIIVKIFVEFSIASETHKAIQALNGR------WFAGR 94
>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 = 36.2 bits (82), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+G LY+ G+ + L+ FS FG I + DP + FV + E A +A+
Sbjct: 38 KGNTLYV--YGEDMTPTLLRGAFSPFGNIIDLSM--DPP---RNCAFVTYEKMESADQAV 90
Query: 370 AEMNGKMIVSKPLYVAVAQRK 390
AE+NG + S L V +A+++
Sbjct: 91 AELNGTQVESVQLKVNIARKQ 111
Score = 35.8 bits (81), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 10/85 (11%)
Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
RK T ++ +++ ++ L FS FGNI+ + + FV +E ESA
Sbjct: 37 RKGNTLYVYGEDMTPTL----LRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESAD 87
Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQ 197
A+ +LNG + Q+ V + RKQ
Sbjct: 88 QAVAELNGTQVESVQLKV-NIARKQ 111
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 36.2 bits (82), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 46/88 (52%), Gaps = 5/88 (5%)
Query: 19 AAGASGNQFLTT---SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGY 75
++G+SG + T + YVG+L FN + +F + + SVR+ RD T + G+ Y
Sbjct: 2 SSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCY 60
Query: 76 VNYANPADAARALDVLNFTPLNNKSIRI 103
V + + D+ + + L ++S+R+
Sbjct: 61 VEF-DEVDSLKEALTYDGALLGDRSLRV 87
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 36.2 bits (82), Expect = 0.059, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 35/65 (53%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
N+F+ NL+ + + +LK E V+ G ++ FG+V+FE+A+D KA+E
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELT 78
Query: 270 NGKKF 274
K F
Sbjct: 79 GLKVF 83
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 35.8 bits (81), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 8/58 (13%)
Query: 120 IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
+FI NL K++ + L FS +G+I+ I FGF+QF+N +S ++AI+
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 75
Score = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 76
>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 = 35.8 bits (81), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 311 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS---GISKGSGFVAFSTPE---E 364
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 365 ASRALAEM 372
A AL M
Sbjct: 63 AQNALHNM 70
Score = 35.4 bits (80), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVE 267
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 268 ALNGKK 273
AL+ K
Sbjct: 66 ALHNMK 71
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.8 bits (81), Expect = 0.074, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK----CFGFVNFENADDAAKAV 266
++V NL +D++ +F +YG I RD D K++ F FV FE+ DA AV
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAI------RDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78
Query: 267 EALNGKKFD 275
+G +D
Sbjct: 79 YGRDGYDYD 87
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
I++ NL I K + D F +G I + G F FV+FE+ A++A+ +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP--FAFVEFEDPRDAEDAVYGRD 82
Query: 180 G 180
G
Sbjct: 83 G 83
Score = 28.9 bits (63), Expect = 7.4, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 18 VAAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRR-SLGYGYV 76
V G +GN +YVG+L ++ + D+F + G + + DL RR + +V
Sbjct: 13 VIRGPAGNN--DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI----DLKNRRGGPPFAFV 66
Query: 77 NYANPADAARAL 88
+ +P DA A+
Sbjct: 67 EFEDPRDAEDAV 78
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 35.8 bits (81), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 10/85 (11%)
Query: 113 RKSGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQ 172
RK T ++ +++ ++ L FS FGNI+ + + FV +E ESA
Sbjct: 13 RKGNTLYVYGEDMTPTL----LRGAFSPFGNIIDLSMDP-----PRNCAFVTYEKMESAD 63
Query: 173 NAIDKLNGMLINDKQVFVGHFLRKQ 197
A+ +LNG + Q+ V + RKQ
Sbjct: 64 QAVAELNGTQVESVQLKV-NIARKQ 87
Score = 35.4 bits (80), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
+G LY+ G+ + L+ FS FG I + DP + FV + E A +A+
Sbjct: 14 KGNTLYV--YGEDMTPTLLRGAFSPFGNIIDLSM--DPP---RNCAFVTYEKMESADQAV 66
Query: 370 AEMNGKMIVSKPLYVAVAQRK 390
AE+NG + S L V +A+++
Sbjct: 67 AELNGTQVESVQLKVNIARKQ 87
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 35.4 bits (80), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 8/58 (13%)
Query: 120 IFIKNLD-KSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAID 176
+FI NL K++ + L FS +G+I+ I FGF+QF+N +S ++AI+
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 55
Score = 32.3 bits (72), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 211 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 56
>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 = 35.4 bits (80), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAV-VMRD-GDGKSKCFGFVNFENADDAAKAV 266
N V ++ L ++ T++D++ +G V +MR+ G+S+ F FV F + DA + +
Sbjct: 2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWM 61
Query: 267 EA 268
EA
Sbjct: 62 EA 63
>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 = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 364
++++ LG+++ E + + F + G I + K P +G KG V+F P
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 365 ASRALAEMNGKMIVSKPLYVAVA 387
A A+ +GK P+ V+ A
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
Score = 28.9 bits (63), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLS--------VRVCRDLSTRRSLGYGYVNYANPA 82
+++V L NVT + D F Q+G + + + + D T + G V++ +P
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 83 DAARALDVLNFTPLNNKSIRIMYS 106
A A+D + + I++ ++
Sbjct: 75 SAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 7/86 (8%)
Query: 31 SLYVGDLDFNVTDSQL----YDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAAR 86
++Y+ +++ + +L Y LFSQ G V+ + + + R G +V + +
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMR---GQAFVIFKELGSSTN 64
Query: 87 ALDVLNFTPLNNKSIRIMYSHRDPSI 112
AL L P K +RI Y+ D I
Sbjct: 65 ALRQLQGFPFYGKPMRIQYAKTDSDI 90
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 7/77 (9%)
Query: 210 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 269
+ KNL + T+++LK++F + + + DGKSK ++ F++ DA K +E
Sbjct: 18 TLLAKNLSFNITEDELKEVFED----ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 270 NGKKFDDRE---WYVGK 283
G + D R +Y G+
Sbjct: 74 QGAEIDGRSVSLYYTGE 90
Score = 28.9 bits (63), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 313 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 372
L KNL +I +++LKE+F + I + G SKG ++ F + +A + L E
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 373 NGKMI 377
G I
Sbjct: 74 QGAEI 78
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 1/89 (1%)
Query: 307 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 366
D Q LY+ NL + + + +LFS+ G SCK++ + + + FV F +A+
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAA 69
Query: 367 RALAEMNGKMIVSKPLYVAVAQRKEERRA 395
ALA MNG+ I+ K + V A +++
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPSSQKS 98
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 48/86 (55%), Gaps = 3/86 (3%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
+LYVG+L +VT+ + LFSQ+G S ++ + ++ Y +V + DAA AL
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 74
Query: 91 LNFTPLNNKSIRIMYSHRDPSIRKSG 116
+N + K +++ ++ PS +KSG
Sbjct: 75 MNGRKILGKEVKVNWA-TTPSSQKSG 99
Score = 28.9 bits (63), Expect = 9.6, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+++ NL + + + FS G SCK+ T+ + + FV+F A A+ +N
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAMN 76
Query: 180 GMLINDKQVFV 190
G I K+V V
Sbjct: 77 GRKILGKEVKV 87
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
+G L++ ++ + +++++E F ++G I + + D +G SKG V + T ++A A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 369 LAEMNGKMIVSKPLYV 384
+NG I+ + + V
Sbjct: 85 KEALNGAEIMGQTIQV 100
Score = 33.9 bits (76), Expect = 0.27, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
+FV ++ E ++++++ F +YG I + + D G SK + V +E A A EAL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 270 NGKK 273
NG +
Sbjct: 89 NGAE 92
Score = 32.7 bits (73), Expect = 0.53, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 109 DPSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 166
+P ++S G I F+ ++ + + + F +G I + + D +G SKG+ V++E
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76
Query: 167 NKESAQNAIDKLNGMLINDKQVFV 190
+ A A + LNG I + + V
Sbjct: 77 THKQALAAKEALNGAEIMGQTIQV 100
>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 = 0.13, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
+I++ N+D + L F G++ I D SG KGF +++F +KES + ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 178 LNGMLINDKQVFV 190
L+ L +Q+ V
Sbjct: 67 LDESLFRGRQIKV 79
Score = 30.0 bits (66), Expect = 3.4, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
S+YVG++D+ T +L F G V V + D + G+ Y+ +++ ++ R
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLA 66
Query: 91 LNFTPLNNKSIRIM 104
L+ + + I+++
Sbjct: 67 LDESLFRGRQIKVI 80
>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 = 0.13, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 119 NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
+I++ N+D + L F G++ I D SG KGF +++F +KES + ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 65
Query: 178 LNGMLINDKQVFV 190
L+ L +Q+ V
Sbjct: 66 LDESLFRGRQIKV 78
Score = 30.0 bits (66), Expect = 3.4, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDV 90
S+YVG++D+ T +L F G V V + D + G+ Y+ +++ ++ R
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLA 65
Query: 91 LNFTPLNNKSIRIM 104
L+ + + I+++
Sbjct: 66 LDESLFRGRQIKVI 79
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 55/114 (48%), Gaps = 14/114 (12%)
Query: 288 SEREQELKGQFEQAMKETVDKFQG-------LNLYIKNLGDSIDDEKLKELFSEFGTITS 340
S RE E KG+ + ET+ F+ +Y+KNL + ++ LK +F + +S
Sbjct: 16 SRRELE-KGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSS 74
Query: 341 --CKVMRD----PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 388
++M D G KG F+ + A++AL E NG ++ KP+ V A+
Sbjct: 75 ETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR 128
Score = 32.7 bits (73), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 31/108 (28%), Positives = 54/108 (50%), Gaps = 13/108 (12%)
Query: 176 DKLNGMLINDKQVFVGHFLRKQERETVAIKTKFN------NVFVKNLDESTTDEDLKKIF 229
D++ I+ +++ G R +E ET+++ + ++VKNL + ++DLK IF
Sbjct: 8 DEMPSECISRRELEKGRISR-EEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIF 66
Query: 230 GEYGTITSAV--VMRD----GDGKSKCFGFVNFENADDAAKAVEALNG 271
G Y +S +M D +G+ K F+ N AAKA++ NG
Sbjct: 67 GRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANG 114
>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 = 34.3 bits (77), Expect = 0.21, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 206 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFE 257
T+ + +FV NL T+E+++K+F +YG + +D K FGF+ E
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLE 59
Score = 33.1 bits (74), Expect = 0.49, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
+F+ NL I + + F +G I D KGFGF++ E + A+ A +L+
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 72
Query: 180 GMLINDKQVFV 190
M + KQ+ V
Sbjct: 73 NMPLRGKQLRV 83
Score = 32.3 bits (72), Expect = 0.85, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 369
Q L++ NL I +E++++LF ++G + +D KG GF+ T A A
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAK 68
Query: 370 AEMNGKMIVSKPLYVAVA 387
E++ + K L V A
Sbjct: 69 VELDNMPLRGKQLRVRFA 86
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 30 TSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALD 89
+ L+VG+L ++T+ ++ LF + G+ V + +D G+G++ A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 69
Query: 90 VLNFTPLNNKSIRIMYSHRDPSI 112
L+ PL K +R+ ++ S+
Sbjct: 70 ELDNMPLRGKQLRVRFACHSASL 92
>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 = 0.22, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 9/86 (10%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 364
+Y++ L DS+ + L + F + G + K P +G KG V++ P
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 365 ASRALAEMNGKMIVSKPLYVAVAQRK 390
A A+ +GK L V++A++K
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 32.0 bits (71), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITS---------AVVMRDGDGKSKCFGFVNFENADD 261
++V+ L++S T +DL F + G + + + GK K V++E+
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 262 AAKAVEALNGKKFDDREWYVGKAQKK 287
A AVE +GK F + V A+KK
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 23/105 (21%), Positives = 46/105 (43%), Gaps = 11/105 (10%)
Query: 19 AAGASGN---QFLTTSLYVGDLDFNVTDSQLYDLFSQVGQV--------LSVRVCRDLST 67
++G+SG+ +++YV L+ +VT L D F Q G V + + D T
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 68 RRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHRDPSI 112
+ G V+Y +P A A++ + +++ + + P +
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 34.3 bits (77), Expect = 0.22, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 69
Query: 269 LNGKKFDDRE 278
L+ KF E
Sbjct: 70 LDNTKFRSHE 79
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 34.3 bits (77), Expect = 0.22, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 69
Query: 269 LNGKKFDDRE 278
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 = 33.9 bits (76), Expect = 0.23, Method: Composition-based stats.
Identities = 21/88 (23%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 310 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 368
+G L++ ++ + +++++E F ++G I + + D +G SKG V + T ++A A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 369 LAEMNGKMIVSKPLYVAVAQRKEERRAR 396
+NG I+ + + V K +R +
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKGPKRVK 158
Score = 33.5 bits (75), Expect = 0.34, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 269
+FV ++ E ++++++ F +YG I + + D G SK + V +E A A EAL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 270 NGKKFDDR----EWYVGKAQKKSEREQE 293
NG + + +W K K+ ++ ++
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVKKSEK 162
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 109 DPSIRKSGTGNI-FIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFE 166
+P ++S G I F+ ++ + + + F +G I + + D +G SKG+ V++E
Sbjct: 63 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122
Query: 167 NKESAQNAIDKLNGMLINDKQVFV 190
+ A A + LNG I + + V
Sbjct: 123 THKQALAAKEALNGAEIMGQTIQV 146
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 33.9 bits (76), Expect = 0.25, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
LY+ LGD+I + L+ F +FG I + V++ + F+ F+T + A A +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKSF 69
Query: 374 GKMIVS 379
K+IV+
Sbjct: 70 NKLIVN 75
Score = 32.7 bits (73), Expect = 0.58, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 28/45 (62%)
Query: 19 AAGASGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCR 63
++G+SG T+LYVG L +T++ L + F Q G++ ++ V +
Sbjct: 2 SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ 46
>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 = 0.25, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 70
Query: 269 LNGKKFDDRE 278
L+ KF E
Sbjct: 71 LDNTKFRSHE 80
>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 = 33.9 bits (76), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 47/96 (48%), Gaps = 15/96 (15%)
Query: 193 FLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK--- 249
LRKQE ++ N V K++D+ E + + G++G + ++ ++ G+ +
Sbjct: 14 LLRKQESTVXVLR---NXVDPKDIDDDLEGE-VTEECGKFGAVNRVIIYQEKQGEEEDAE 69
Query: 250 --CFGFVNFENADDAAKAVEALNGKKFDDREWYVGK 283
FV F A + KA++ALNG+ W+ G+
Sbjct: 70 IIVKIFVEFSIASETHKAIQALNGR------WFAGR 99
>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 = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 12/97 (12%)
Query: 147 CKIATDGSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFVGH----------FLRK 196
C G + F + QF N + N DKL L K++++ + +RK
Sbjct: 734 CNAIAQGGEEEWDFAWEQFRNA-TLVNEADKLRAALACSKELWILNRYLSYTLNPDLIRK 792
Query: 197 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG 233
Q+ + I NNV + L + KK+F +YG
Sbjct: 793 QDATSTIISIT-NNVIGQGLVWDFVQSNWKKLFNDYG 828
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.1 bits (74), Expect = 0.43, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQS-KGFGFVQFENKESAQNAID 176
IF+ + + L + F FG + + D Q +GFGF+ FE+++S A++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Score = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 15/72 (20%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 32 LYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVL 91
++VG + N +++L + F + G V V + D +R G+G++ + + +A++ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 92 NFTPLNNKSIRI 103
+F + K + +
Sbjct: 72 HFHDIMGKKVEV 83
>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 = 32.3 bits (72), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 48/97 (49%), Gaps = 6/97 (6%)
Query: 97 NNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFG--NILSCKIATD-G 153
NNK+ I+Y++ R++ +++ + + L S G +++ K A +
Sbjct: 38 NNKTPAILYTYSGLRNRRAA---VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94
Query: 154 SGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
+GQSKG+ V ++ S ++ L G ++N ++V V
Sbjct: 95 NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDV 131
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 23 SGNQFLTTSLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRSLGYGYVNYAN 80
SG + ++YVG + TD QL + +G V+ ++ + + +S GY V A+
Sbjct: 49 SGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVAS 108
Query: 81 PADAARALDVLNFTPLNNKSIRIMYSHR 108
+ L++L LN + + + + R
Sbjct: 109 ENSVHKLLELLPGKVLNGEKVDVRPATR 136
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 314 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 373
L I+N+ + E L L ++G + SC+ + S + + V +S+ ++A +AL ++N
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVN--VTYSSKDQARQALDKLN 75
Query: 374 G 374
G
Sbjct: 76 G 76
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 122 IKNLDKSIDHKALHDTFSSFGNILSC-KIATDGSGQSKGFGFVQFENKESAQNAIDKLNG 180
I+N+ + + L +G + SC ++ TD V + +K+ A+ A+DKLNG
Sbjct: 20 IRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALDKLNG 76
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 49/108 (45%), Gaps = 10/108 (9%)
Query: 106 SHRDPSIRKSGTG---NIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGF 162
SH D + +G I ++NL + LH FS FG +L KI T + ++
Sbjct: 19 SHMDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL--KIIT-FTKNNQFQAL 75
Query: 163 VQFENKESAQNAIDKLNGMLINDKQVFVGHFLRKQERETVAIKTKFNN 210
+Q+ + SAQ+A L+G I + LR + ++ K+NN
Sbjct: 76 LQYADPVSAQHAKLSLDGQNIYNACC----TLRIDFSKLTSLNVKYNN 119
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
+FV L T +E +++ FG +G + S + M + K + F F+ F+ + K +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
Score = 31.2 bits (69), Expect = 1.6, Method: Composition-based stats.
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
IF+ L + + + F FG + S ++ D + + +GF F+ F+ +E + ++K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>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 = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 211 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVE 267
+FV L T +E +++ FG +G + S + M + K + F F+ F+ + K +E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDG-SGQSKGFGFVQFENKESAQNAIDK 177
IF+ L + + + F FG + S ++ D + + +GF F+ F+ +E + ++K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>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 = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 132 KALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQVFV 190
KAL FS G +++ + D +G++KGF FV+ + A+ I +G ++ K
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLF 86
Query: 191 GHFLRKQER 199
+ ++ ER
Sbjct: 87 LYTMKDVER 95
Score = 29.3 bits (64), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 225 LKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK 283
L +F + G + + + + GK+K F FV + +DA K +++ +GK+ D +
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLY 88
Query: 284 AQKKSER 290
K ER
Sbjct: 89 TMKDVER 95
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 225 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY 280
+ KIF ++G IT+ + DGK+K + F+ + + A AV+ +G K D + +
Sbjct: 24 IHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>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 = 2.0, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 225 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY 280
+ KIF ++G IT+ + DGK+K + F+ + + A AV+ +G K D + +
Sbjct: 38 IHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 18 VAAGASGNQFLT-----TSLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRS 70
V GA+ N T +LY+G+L + TD L + +G +L ++ + + +S
Sbjct: 52 VGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQS 111
Query: 71 LGYGYVNYANPADAARALDVL 91
G+ V + A + + +D+L
Sbjct: 112 KGFALVGVGSEASSKKLMDLL 132
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 31 SLYVGDLDFNVTDSQLYDLFSQVG--QVLSVRVCRDLSTRRSLGYGYVNYANPADAARAL 88
+LY+G+L + TD L + +G +L ++ + + +S G+ V + A + + +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 89 DVL 91
D+L
Sbjct: 63 DLL 65
>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 = 2.4, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 213 VKNLDESTTDEDLKKIFGEYGTITSAV-VMRDGDGKSKCFGFVNFENADDAAKAVEALNG 271
+ N+ S T D+ + +AV V+ D +G+ V F+N DDA K+ E L+
Sbjct: 20 ITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS-ERLHR 78
Query: 272 KKFDDREWYVGKAQKKSEREQE 293
KK + RE +V + RE E
Sbjct: 79 KKLNGREAFVHVVTLEDMREIE 100
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 325 DEKLKELFSE----FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 380
DE +E+F+E +G + V + G+ +V F E+A +A+ ++N + +
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 381 PLYVAVA 387
P++ ++
Sbjct: 97 PIHAELS 103
>pdb|3UX8|A Chain A, Crystal Structure Of Uvra
Length = 670
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 347 PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 401
P G +G VA TPEE + G+ + KP+ E RAR+QA++
Sbjct: 620 PEGGDRGGQIVAVGTPEEVAEVKESHTGRYL--KPIL-------ERDRARMQARY 665
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
SG+ I +KNL + + + +HD + ++ C + ++K FV N E AQNA
Sbjct: 3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYV-----DRNKRTAFVTLLNGEQAQNA 56
Query: 175 I 175
I
Sbjct: 57 I 57
>pdb|3UWX|A Chain A, Crystal Structure Of Uvra-Uvrb Complex
Length = 972
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: 347 PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 401
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 = 3.6, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 7/91 (7%)
Query: 120 IFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNAIDKLN 179
I ++NL + LH FS FG +L KI T + ++ +Q+ + SAQ+A L+
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVL--KIIT-FTKNNQFQALLQYADPVSAQHAKLSLD 105
Query: 180 GMLINDKQVFVGHFLRKQERETVAIKTKFNN 210
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 = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 209 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 268
+ VFV E T E+L++ F +YG + + + + F FV F ADD K ++
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTF--ADD--KVAQS 63
Query: 269 LNGK 272
L G+
Sbjct: 64 LCGE 67
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 115 SGTGNIFIKNLDKSIDHKALHDTFSSFGNILSCKIATDGSGQSKGFGFVQFENKESAQNA 174
SG+ I I+ L + ++ +HD S + + C + + KG FV N E A+ A
Sbjct: 3 SGSSGILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD-----KYKGTAFVTLLNGEQAEAA 56
Query: 175 IDKLNGMLINDKQVFV 190
I+ + + ++++ V
Sbjct: 57 INTFHQSRLRERELSV 72
>pdb|1VPV|A Chain A, Crystal Structure Of A Degv Lipid Binding Protein (Tm1468)
From Thermotoga Maritima At 2.45 A Resolution
pdb|1VPV|B Chain B, Crystal Structure Of A Degv Lipid Binding Protein (Tm1468)
From Thermotoga Maritima At 2.45 A Resolution
Length = 300
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 61/144 (42%), Gaps = 11/144 (7%)
Query: 25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
N+ YV + D+ V ++ VG +L +RVC + + Y V A
Sbjct: 167 NKDFKAIFYVSNFDYLVKGGRVSKFQGFVGNLLKIRVCLHIENGELIPYRKVRGDKKAIE 226
Query: 85 ARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
A + TP +K +R++ H D ++G + + L KS ++ + + S G +
Sbjct: 227 ALIEKLREDTPEGSK-LRVIGVHAD---NEAGVVEL-LNTLRKS--YEVVDEIISPXGKV 279
Query: 145 LSCKIATDGSGQSKGFGFVQFENK 168
++ + G G + GFG E K
Sbjct: 280 ITTHV---GPG-TVGFGIEVLERK 299
>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 = 6.0, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 132 KALHDTFSSFGNILSCKIATD-GSGQSKGFGFVQFENKESAQNAIDKLNGMLINDKQ 187
KAL FS G +++ + D +G++KGF FV+ + A+ I +G ++ K
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH 83
Score = 29.3 bits (64), Expect = 6.7, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 225 LKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD 275
L +F + G + + + + GK+K F FV + +DA K +++ +GK+ D
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|3O8Y|A Chain A, Stable-5-Lipoxygenase
pdb|3O8Y|B Chain B, Stable-5-Lipoxygenase
Length = 691
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 33/78 (42%)
Query: 49 LFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR 108
+F ++ +S RV GY ++N ANP R ++ P+ + + +
Sbjct: 228 IFVKISNTISERVMNHWQEDLMFGYQFLNGANPVLIRRCTELPEKLPVTTEMVECSLERQ 287
Query: 109 DPSIRKSGTGNIFIKNLD 126
++ GNIFI + +
Sbjct: 288 LSLEQEVQQGNIFIVDFE 305
>pdb|3V98|A Chain A, S663d Stable-5-Lox
pdb|3V98|B Chain B, S663d Stable-5-Lox
pdb|3V99|A Chain A, S663d Stable-5-Lox In Complex With Arachidonic Acid
pdb|3V99|B Chain B, S663d Stable-5-Lox In Complex With Arachidonic Acid
Length = 691
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 33/78 (42%)
Query: 49 LFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR 108
+F ++ +S RV GY ++N ANP R ++ P+ + + +
Sbjct: 228 IFVKISNTISERVMNHWQEDLMFGYQFLNGANPVLIRRCTELPEKLPVTTEMVECSLERQ 287
Query: 109 DPSIRKSGTGNIFIKNLD 126
++ GNIFI + +
Sbjct: 288 LSLEQEVQQGNIFIVDFE 305
>pdb|3V92|B Chain B, S663a Stable-5-Lox
pdb|3V92|A Chain A, S663a Stable-5-Lox
Length = 691
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 33/78 (42%)
Query: 49 LFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADAARALDVLNFTPLNNKSIRIMYSHR 108
+F ++ +S RV GY ++N ANP R ++ P+ + + +
Sbjct: 228 IFVKISNTISERVMNHWQEDLMFGYQFLNGANPVLIRRCTELPEKLPVTTEMVECSLERQ 287
Query: 109 DPSIRKSGTGNIFIKNLD 126
++ GNIFI + +
Sbjct: 288 LSLEQEVQQGNIFIVDFE 305
>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: 264 KAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQ 310
K +E + + DR + + + K+E + E K FEQ ++ETV ++
Sbjct: 289 KDIEYVTDRLGHDRRYAINAEKXKNEFDWEPKYTFEQGLQETVQWYE 335
>pdb|1MGP|A Chain A, Hypothetical Protein Tm841 From Thermotoga Maritima
Reveals Fatty Acid Binding Function
Length = 313
Score = 29.3 bits (64), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 61/144 (42%), Gaps = 11/144 (7%)
Query: 25 NQFLTTSLYVGDLDFNVTDSQLYDLFSQVGQVLSVRVCRDLSTRRSLGYGYVNYANPADA 84
N+ YV + D+ V ++ VG +L +RVC + + Y V A
Sbjct: 180 NKDFKAIFYVSNFDYLVKGGRVSKFQGFVGNLLKIRVCLHIENGELIPYRKVRGDKKAIE 239
Query: 85 ARALDVLNFTPLNNKSIRIMYSHRDPSIRKSGTGNIFIKNLDKSIDHKALHDTFSSFGNI 144
A + TP +K +R++ H D ++G + + L KS ++ + + S G +
Sbjct: 240 ALIEKLREDTPEGSK-LRVIGVHAD---NEAGVVEL-LNTLRKS--YEVVDEIISPXGKV 292
Query: 145 LSCKIATDGSGQSKGFGFVQFENK 168
++ + G G + GFG E K
Sbjct: 293 ITTHV---GPG-TVGFGIEVLERK 312
>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 = 9.0, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 15/87 (17%)
Query: 216 LDESTTDEDLK----KIFGEYGTITSAVVMRDGDGKSK-----CFGFVNFENADDAAKAV 266
+D D+DL+ + G++G + ++ ++ G+ + FV F A + KA+
Sbjct: 133 VDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAI 192
Query: 267 EALNGKKFDDREWYVGKAQKKSEREQE 293
+ALNG+ W+ G+ +QE
Sbjct: 193 QALNGR------WFAGRKVVAEVYDQE 213
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
0.316 0.132 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,676,620
Number of Sequences: 62578
Number of extensions: 636701
Number of successful extensions: 3003
Number of sequences better than 100.0: 267
Number of HSP's better than 100.0 without gapping: 168
Number of HSP's successfully gapped in prelim test: 99
Number of HSP's that attempted gapping in prelim test: 2051
Number of HSP's gapped (non-prelim): 772
length of query: 593
length of database: 14,973,337
effective HSP length: 104
effective length of query: 489
effective length of database: 8,465,225
effective search space: 4139495025
effective search space used: 4139495025
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)