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= 006641
(637 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 226 bits (576), Expect = 3e-59, Method: Compositional matrix adjust.
Identities = 107/176 (60%), Positives = 132/176 (75%), Gaps = 1/176 (0%)
Query: 25 YGNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAAN 84
Y SLYVGDL +V E+ LY+ FS ++S+RVCRD R SLGYAYVN+ P DA
Sbjct: 8 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Query: 85 AKEALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLS 144
A + +NF I GKP+RIM+S RDPS+RKSG GN+FIKNLD SIDNKAL DTF+AFG +LS
Sbjct: 68 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 127
Query: 145 CKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQ 200
CKV D NG SKGYGFV FE +EAA+ AI+ +NGML+ND++V+VG F R+ER +
Sbjct: 128 CKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182
Score = 94.0 bits (232), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 59/190 (31%), Positives = 102/190 (53%), Gaps = 6/190 (3%)
Query: 107 DPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFEN 165
+PS ++++ +L + L + F+ G +LS +V D +S GY +V F+
Sbjct: 2 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 61
Query: 166 EEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKK 225
A+ A+ +N +I K V + R + V N+++ NL +++ ++ L
Sbjct: 62 PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYD 117
Query: 226 IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNGTTNNDKVWYVGRAQKR 285
F FG I S V+ D +G S+ +GFV+F++ +AA A+EK+NG ND+ +VGR + R
Sbjct: 118 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 176
Query: 286 AEREADLRAK 295
EREA+L A+
Sbjct: 177 KEREAELGAR 186
Score = 94.0 bits (232), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 65/193 (33%), Positives = 102/193 (52%), Gaps = 18/193 (9%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVE 265
++YV +L VT+ L + F G I S V +D +S + +VNFQ P A A++
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
+N K + +Q R+ LR K N+++KNLD SI+++
Sbjct: 71 TMNFDVIKGKPVRIMWSQ----RDPSLR------------KSGVGNIFIKNLDKSIDNKA 114
Query: 326 LKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVA 385
L + FS FG I SCKV+ D++G SKG GF F E A RA+ +MNG ++ + ++V
Sbjct: 115 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 173
Query: 386 QRKEERKARLQAQ 398
+ ++ER+A L A+
Sbjct: 174 KSRKEREAELGAR 186
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 226 bits (575), Expect = 3e-59, Method: Compositional matrix adjust.
Identities = 107/176 (60%), Positives = 132/176 (75%), Gaps = 1/176 (0%)
Query: 25 YGNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAAN 84
Y SLYVGDL +V E+ LY+ FS ++S+RVCRD R SLGYAYVN+ P DA
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 85 AKEALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLS 144
A + +NF I GKP+RIM+S RDPS+RKSG GN+FIKNLD SIDNKAL DTF+AFG +LS
Sbjct: 73 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 132
Query: 145 CKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQ 200
CKV D NG SKGYGFV FE +EAA+ AI+ +NGML+ND++V+VG F R+ER +
Sbjct: 133 CKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 187
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 59/193 (30%), Positives = 104/193 (53%), Gaps = 6/193 (3%)
Query: 107 DPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFEN 165
+PS ++++ +L + L + F+ G +LS +V D +S GY +V F+
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 166 EEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKK 225
A+ A+ +N +I K V + R + V N+++ NL +++ ++ L
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYD 122
Query: 226 IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNGTTNNDKVWYVGRAQKR 285
F FG I S V+ D +G S+ +GFV+F++ +AA A+EK+NG ND+ +VGR + R
Sbjct: 123 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
Query: 286 AEREADLRAKFEQ 298
EREA+L A+ ++
Sbjct: 182 KEREAELGARAKE 194
Score = 94.7 bits (234), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 65/193 (33%), Positives = 102/193 (52%), Gaps = 18/193 (9%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVE 265
++YV +L VT+ L + F G I S V +D +S + +VNFQ P A A++
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
+N K + +Q R+ LR K N+++KNLD SI+++
Sbjct: 76 TMNFDVIKGKPVRIMWSQ----RDPSLR------------KSGVGNIFIKNLDKSIDNKA 119
Query: 326 LKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVA 385
L + FS FG I SCKV+ D++G SKG GF F E A RA+ +MNG ++ + ++V
Sbjct: 120 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178
Query: 386 QRKEERKARLQAQ 398
+ ++ER+A L A+
Sbjct: 179 KSRKEREAELGAR 191
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 132 bits (331), Expect = 7e-31, Method: Composition-based stats.
Identities = 63/94 (67%), Positives = 77/94 (81%), Gaps = 1/94 (1%)
Query: 107 DPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENE 166
DPS+RKSG GN+FIKNLD SIDNKAL DTF+AFG +LSCKV D NG SKGYGFV FE +
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 167 EAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQ 200
EAA+ AI+ +NGML+ND++V+VG F R+ER +
Sbjct: 62 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 74.7 bits (182), Expect = 1e-13, Method: Composition-based stats.
Identities = 36/84 (42%), Positives = 57/84 (67%), Gaps = 1/84 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNE 369
N+++KNLD SI+++ L + FS FG I SCKV+ D++G SKG GF F E A RA+ +
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEK 70
Query: 370 MNGKMIGRKPLYVAVAQRKEERKA 393
MNG ++ + ++V + ++ER+A
Sbjct: 71 MNGMLLNDRKVFVGRFKSRKEREA 94
Score = 68.9 bits (167), Expect = 9e-12, Method: Composition-based stats.
Identities = 34/84 (40%), Positives = 56/84 (66%), Gaps = 1/84 (1%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKL 267
N+++ NL +++ ++ L F FG I S V+ D +G S+ +GFV+F++ +AA A+EK+
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 268 NGTTNNDKVWYVGRAQKRAEREAD 291
NG ND+ +VGR + R EREA+
Sbjct: 72 NGMLLNDRKVFVGRFKSRKEREAE 95
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 126 bits (316), Expect = 5e-29, Method: Composition-based stats.
Identities = 64/108 (59%), Positives = 80/108 (74%), Gaps = 3/108 (2%)
Query: 114 GYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAI 173
G GN+FIKNLD SIDNKAL DTF+AFG +LSCKV D NG SKGYGFV FE +EAA+ AI
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 174 KMLNGMLINDKQVYVGLFVRRQERAQQ--NVSPKFTNVYVNNLAETVT 219
+ +NGML+ND++V+VG F R+ER + + +FTNVY+ N T
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110
Score = 77.8 bits (190), Expect = 2e-14, Method: Composition-based stats.
Identities = 39/92 (42%), Positives = 61/92 (66%), Gaps = 1/92 (1%)
Query: 307 LKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
L N+++KNLD SI+++ L + FS FG I SCKV+ D++G SKG GF F E A RA
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERA 61
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARLQAQ 398
+ +MNG ++ + ++V + ++ER+A L A+
Sbjct: 62 IEKMNGMLLNDRKVFVGRFKSRKEREAELGAR 93
Score = 72.4 bits (176), Expect = 8e-13, Method: Composition-based stats.
Identities = 40/110 (36%), Positives = 67/110 (60%), Gaps = 11/110 (10%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKL 267
N+++ NL +++ ++ L F FG I S V+ D +G S+ +GFV+F++ +AA A+EK+
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 268 NGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNL 317
NG ND+ +VGR + R EREA+L A+ ++ N+Y+KN
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGARAKE----------FTNVYIKNF 105
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 119 bits (297), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 58/95 (61%), Positives = 77/95 (81%), Gaps = 4/95 (4%)
Query: 299 ERISRYEKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFS 358
+RI+RY+ + NLY+KNLDD I+DE+L++ FS FGTITS KVM+ + G SKG GF FS
Sbjct: 8 DRITRYQVV---NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKGFGFVCFS 63
Query: 359 MPEEATRALNEMNGKMIGRKPLYVAVAQRKEERKA 393
PEEAT+A+ EMNG+++ KPLYVA+AQRKEER++
Sbjct: 64 SPEEATKAVTEMNGRIVATKPLYVALAQRKEERQS 98
Score = 76.3 bits (186), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 40/83 (48%), Positives = 54/83 (65%), Gaps = 1/83 (1%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKL 267
N+YV NL + + DE L+K F FGTITSA VM + G+S+ FGFV F SP+ A AV ++
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 268 NGTTNNDKVWYVGRAQKRAEREA 290
NG K YV AQ++ ER++
Sbjct: 76 NGRIVATKPLYVALAQRKEERQS 98
Score = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 35/81 (43%), Positives = 54/81 (66%), Gaps = 1/81 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
N+++KNLD ID++ L F+ FGT+ S KV ++ G+SKG+GFV F + E A A+ +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 177 NGMLINDKQVYVGLFVRRQER 197
NG ++ K +YV L R++ER
Sbjct: 76 NGRIVATKPLYVALAQRKEER 96
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 3/90 (3%)
Query: 25 YGNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAAN 84
Y V+LYV +L+ +++ +L FS + S +V + + S G+ +V +S+P++A
Sbjct: 13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGR--SKGFGFVCFSSPEEATK 70
Query: 85 AKEALNFMPINGKPIRIMYSHRDPSIRKSG 114
A +N + KP+ + + R R+SG
Sbjct: 71 AVTEMNGRIVATKPLYVALAQRKEE-RQSG 99
>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 = 94.0 bits (232), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 84/154 (54%), Gaps = 3/154 (1%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G +L V L QN+ + +L LFS + +V S ++ RD+ SLGY +VNY +DA A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 86 KEALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSC 145
LN + + K I++ Y+ + K N++I L ++ K + D F+ FG +++
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKD--ANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 146 KVAID-SNGQSKGYGFVQFENEEAAQNAIKMLNG 178
+V +D + G S+G F++F+ A+ AI NG
Sbjct: 119 RVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 52/168 (30%), Positives = 83/168 (49%), Gaps = 20/168 (11%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVE 265
TN+ VN L + +T ++L+ +F G + SA +++D G S +GFVN+ + A A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
LNG K V A+ +E +K ANLY+ L ++ +
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE------------------VIKDANLYISGLPRTMTQKD 104
Query: 326 LKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNG 372
++++FS FG I + +V+VDQ G S+G F F EA A+ NG
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 47/158 (29%), Positives = 77/158 (48%), Gaps = 8/158 (5%)
Query: 114 GYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNA 172
G N+ + L ++ L F++ G V S K+ D G S GYGFV + + A+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 173 IKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGT 232
I LNG+ + K + V + R ++ N+Y++ L T+T +D++ +F FG
Sbjct: 61 INTLNGLRLQSKTIKVS-YARPSSEVIKDA-----NLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 233 ITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
I ++ V+ D + G SR F+ F A A+ NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALN 368
NL + L ++ ++L+ LFS G + S K++ D+ G S G GF + ++A RA+N
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 369 EMNGKMIGRKPLYVAVAQRKEE 390
+NG + K + V+ A+ E
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE 84
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 94.0 bits (232), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 84/154 (54%), Gaps = 3/154 (1%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G +L V L QN+ + +L LFS + +V S ++ RD+ SLGY +VNY +DA A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 86 KEALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSC 145
LN + + K I++ Y+ + K N++I L ++ K + D F+ FG +++
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKD--ANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 146 KVAID-SNGQSKGYGFVQFENEEAAQNAIKMLNG 178
+V +D + G S+G F++F+ A+ AI NG
Sbjct: 119 RVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 52/168 (30%), Positives = 83/168 (49%), Gaps = 20/168 (11%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVE 265
TN+ VN L + +T ++L+ +F G + SA +++D G S +GFVN+ + A A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
LNG K V A+ +E +K ANLY+ L ++ +
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE------------------VIKDANLYISGLPRTMTQKD 104
Query: 326 LKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNG 372
++++FS FG I + +V+VDQ G S+G F F EA A+ NG
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 47/158 (29%), Positives = 77/158 (48%), Gaps = 8/158 (5%)
Query: 114 GYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNA 172
G N+ + L ++ L F++ G V S K+ D G S GYGFV + + A+ A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 173 IKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGT 232
I LNG+ + K + V + R ++ N+Y++ L T+T +D++ +F FG
Sbjct: 61 INTLNGLRLQSKTIKVS-YARPSSEVIKDA-----NLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 233 ITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
I ++ V+ D + G SR F+ F A A+ NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALN 368
NL + L ++ ++L+ LFS G + S K++ D+ G S G GF + ++A RA+N
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 369 EMNGKMIGRKPLYVAVAQRKEE 390
+NG + K + V+ A+ E
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE 84
>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 = 92.0 bits (227), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 49/151 (32%), Positives = 85/151 (56%), Gaps = 5/151 (3%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L V L QN+ + + LF + ++ S ++ RD+ SLGY +VNY +P+DA A L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 90 NFMPINGKPIRIMYSH-RDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVA 148
N + + K I++ Y+ SIR + N+++ L ++ K L F+ +G +++ ++
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDA---NLYVSGLPKTMTQKELEQLFSQYGRIITSRIL 121
Query: 149 IDS-NGQSKGYGFVQFENEEAAQNAIKMLNG 178
+D G S+G GF++F+ A+ AIK LNG
Sbjct: 122 VDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 87.0 bits (214), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 53/169 (31%), Positives = 87/169 (51%), Gaps = 20/169 (11%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVE 265
TN+ VN L + +T E+ + +FG G I S +++D G+S +GFVN+ P A A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
LNG K V A+ + ++ ANLY+ L ++ ++
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMTQKE 104
Query: 326 LKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNGK 373
L++LFS++G I + +++VDQ G S+G GF F EA A+ +NG+
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 79.0 bits (193), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 50/155 (32%), Positives = 83/155 (53%), Gaps = 8/155 (5%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKM 175
N+ + L ++ + F + G + SCK+ D GQS GYGFV + + + A+ AI
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 176 LNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFG-TIT 234
LNG+ + K + V + R + S + N+YV+ L +T+T ++L+++F +G IT
Sbjct: 64 LNGLRLQTKTIKVS-YAR-----PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 235 SAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
S I++ G SR GF+ F A A++ LNG
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALN 368
NL + L ++ E+ + LF G I SCK++ D+ G S G GF + P++A +A+N
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 369 EMNGKMIGRKPLYVAVAQ 386
+NG + K + V+ A+
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
+ +LYV L + + + +L LFSQ ++++ R+ DQ S G ++ + +A A
Sbjct: 88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Query: 87 EALNFMPING--KPIRIMYS 104
+ LN +G +PI + ++
Sbjct: 148 KGLNGQKPSGATEPITVKFA 167
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 91.7 bits (226), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 49/153 (32%), Positives = 86/153 (56%), Gaps = 5/153 (3%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKE 87
+L V L QN+ + + LF + + S ++ RD+ SLGY +VNYS+P DA A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 88 ALNFMPINGKPIRIMYSH-RDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCK 146
LN + + K I++ Y+ SIR + N+++ L ++ K + F+ +G +++ +
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASIRDA---NLYVSGLPKTMSQKEMEQLFSQYGRIITSR 121
Query: 147 VAID-SNGQSKGYGFVQFENEEAAQNAIKMLNG 178
+ +D + G S+G GF++F+ A+ AIK LNG
Sbjct: 122 ILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 86.3 bits (212), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 55/179 (30%), Positives = 93/179 (51%), Gaps = 24/179 (13%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVE 265
TN+ VN L + +T ++ K +FG G I S +++D G+S +GFVN+ P+ A A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
LNG K V A+ + ++ ANLY+ L +++ ++
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMSQKE 106
Query: 326 LKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVA 383
+++LFS++G I + ++++DQ G S+G GF F EA A+ +NG+ KPL A
Sbjct: 107 MEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ----KPLGAA 161
Score = 76.6 bits (187), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 48/155 (30%), Positives = 81/155 (52%), Gaps = 8/155 (5%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKM 175
N+ + L ++ F + G + SCK+ D GQS GYGFV + + A AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 176 LNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFG-TIT 234
LNG+ + K + V + R + S + N+YV+ L +T++ ++++++F +G IT
Sbjct: 66 LNGLKLQTKTIKVS-YAR-----PSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIIT 119
Query: 235 SAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
S I++ + G SR GF+ F A A++ LNG
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALN 368
NL + L ++ ++ K LF G I SCK++ D+ G S G GF +S P +A +A+N
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 369 EMNGKMIGRKPLYVAVAQ 386
+NG + K + V+ A+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 36/64 (56%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
+ +LYV L + +++ ++ LFSQ ++++ R+ DQ+ S G ++ + +A A
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 87 EALN 90
+ LN
Sbjct: 150 KGLN 153
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 86.7 bits (213), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 52/154 (33%), Positives = 81/154 (52%), Gaps = 8/154 (5%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKM 175
N+ + L + ++ L F A G + +C++ D G S GY FV F +E +Q AIK+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 176 LNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITS 235
LNG+ + +K++ V E S K TN+YV NL T+TD+ L IFG +G+I
Sbjct: 65 LNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 236 AIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKLN 268
+++D G+ R FV + + A A+ LN
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 81/155 (52%), Gaps = 3/155 (1%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N +L V L Q++ + +LY LF + + + R+ RD S GYA+V++++ D+ A
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 87 EALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCK 146
+ LN + + K +++ Y+ P N+++ NL +I + L F +G+++
Sbjct: 63 KVLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120
Query: 147 VAIDS-NGQSKGYGFVQFENEEAAQNAIKMLNGML 180
+ D G+ +G FV++ E AQ AI LN ++
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Score = 75.9 bits (185), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 54/183 (29%), Positives = 90/183 (49%), Gaps = 22/183 (12%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVE 265
TN+ VN L + +TD +L +F G I + +M+D G S + FV+F S + A++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
LNG T +K V A+ E +K NLY+ NL +I D++
Sbjct: 64 VLNGITVRNKRLKVSYARPGGE------------------SIKDTNLYVTNLPRTITDDQ 105
Query: 326 LKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNGKMI--GRKPLYV 382
L +F ++G+I ++ D+ G +G F ++ EEA A++ +N + G +PL V
Sbjct: 106 LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Query: 383 AVA 385
+A
Sbjct: 166 RLA 168
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALN 368
NL + L + D +L LF G I +C++M D + G+S G F F+ ++ RA+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 369 EMNGKMIGRKPLYVAVAQ 386
+NG + K L V+ A+
Sbjct: 64 VLNGITVRNKRLKVSYAR 81
>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 = 85.5 bits (210), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 52/154 (33%), Positives = 80/154 (51%), Gaps = 8/154 (5%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKM 175
N+ + L ++ L F A G + +C++ D G S GY FV F +E +Q AIK+
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 176 LNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITS 235
LNG+ + +K++ V E S K TN+YV NL T+TD+ L IFG +G+I
Sbjct: 76 LNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 129
Query: 236 AIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKLN 268
+++D G+ R FV + + A A+ LN
Sbjct: 130 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 80/155 (51%), Gaps = 3/155 (1%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N +L V L Q+ + +LY LF + + + R+ RD S GYA+V++++ D+ A
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 87 EALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCK 146
+ LN + + K +++ Y+ P N+++ NL +I + L F +G+++
Sbjct: 74 KVLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 131
Query: 147 VAIDS-NGQSKGYGFVQFENEEAAQNAIKMLNGML 180
+ D G+ +G FV++ E AQ AI LN ++
Sbjct: 132 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
Score = 73.2 bits (178), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 53/184 (28%), Positives = 89/184 (48%), Gaps = 22/184 (11%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVE 265
TN+ VN L + TD +L +F G I + + +D G S + FV+F S + A++
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
LNG T +K V A+ E +K NLY+ NL +I D++
Sbjct: 75 VLNGITVRNKRLKVSYARPGGE------------------SIKDTNLYVTNLPRTITDDQ 116
Query: 326 LKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNGKMI--GRKPLYV 382
L +F ++G+I ++ D+ G +G F ++ EEA A++ +N + G +PL V
Sbjct: 117 LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 176
Query: 383 AVAQ 386
+A+
Sbjct: 177 RLAE 180
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 45/154 (29%), Positives = 83/154 (53%), Gaps = 2/154 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
LYVG+L++ + E L F + ++++ D++ ++ + YA+V Y DA A + L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKN-VNYAFVEYHQSHDANIALQTL 61
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAI 149
N I ++I ++ + N+F+ +L+ ++D++ L + F F + LS V
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 150 D-SNGQSKGYGFVQFENEEAAQNAIKMLNGMLIN 182
D G S+GYGFV F +++ AQNA+ + G +N
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 155
Score = 74.7 bits (182), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 49/153 (32%), Positives = 77/153 (50%), Gaps = 5/153 (3%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+++ NLD +I L F G + + K+ ID N ++ Y FV++ A A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAI 237
G I + V + ++QQ+ S N++V +L V DE L+ F F + S
Sbjct: 63 GKQIENNIVKINWAF----QSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Query: 238 VMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
VM D G SR +GFV+F S D A A++ + G
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG 151
Score = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 50/181 (27%), Positives = 92/181 (50%), Gaps = 19/181 (10%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
+YV NL + +T++ LK+ F G I + +M D + K+ + FV + A A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 269 GTTNNDKVWYVGRAQKRAERE-ADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKLK 327
G K+ E + F+ ++ S + NL++ +L+ +++DE L+
Sbjct: 63 G--------------KQIENNIVKINWAFQSQQSSSDDTF---NLFVGDLNVNVDDETLR 105
Query: 328 ELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVAQ 386
F +F + S VM D Q G S+G GF +F+ ++A A++ M G+ + +PL + A
Sbjct: 106 NAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Query: 387 R 387
+
Sbjct: 166 K 166
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 46/78 (58%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+L+VGDL NV++ L + F +S V D SS GY +V++++ DA NA ++
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 89 LNFMPINGKPIRIMYSHR 106
+ +NG+P+RI ++ +
Sbjct: 149 MQGQDLNGRPLRINWAAK 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 = 75.9 bits (185), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 46/177 (25%), Positives = 92/177 (51%), Gaps = 17/177 (9%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
V++ ++ + + FA FG + S ++ DS + KG+ FV++E EAAQ A++ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 177 NGMLINDKQVYVG----------LFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKI 226
N +++ + + VG + + E A+ F +YV ++ + ++D+D+K +
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEAR-----AFNRIYVASVHQDLSDDDIKSV 145
Query: 227 FGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTNNDKVWYVGRA 282
F FG I SA + +D + GK + +GF+ ++ ++ AV +N + VG+A
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 39/170 (22%), Positives = 82/170 (48%), Gaps = 10/170 (5%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
+YVG + + E + F+ + S+ + D G+A+V Y P+ A A E +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 90 NFMPINGKPIRIM----YSHRDPSIRK-----SGYGNVFIKNLDTSIDNKALCDTFAAFG 140
N + + G+ I++ P I + + +++ ++ + + + F AFG
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 141 TVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVG 189
+ S +A D + G+ KGYGF+++E +++Q+A+ +N + + + VG
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 200
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 79/168 (47%), Gaps = 9/168 (5%)
Query: 206 FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAV 264
+ VYV ++ + ++ +++ F FG I S + DS K + F FV ++ P+AA A+
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 265 EKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDE 324
E++N + VGR + + + E+ R +Y+ ++ ++D+
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN-------RIYVASVHQDLSDD 140
Query: 325 KLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEMN 371
+K +F FG I S + D G KG GF + + + A++ MN
Sbjct: 141 DIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFS-KGSGFAAFSMPEEATRALN 368
+ +Y+ ++ + ++ +++ F+ FG I S + D KG F + +PE A AL
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 369 EMNGKMIGRKPLYV 382
+MN M+G + + V
Sbjct: 89 QMNSVMLGGRNIKV 102
>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum
Aevestium Poly(A)-Binding Protein
Length = 85
Score = 75.5 bits (184), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 36/52 (69%), Positives = 43/52 (82%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P+ + MLGE LYPLV+ +E A+KVTGMLLEMDQTEVLHL+ESP+ALK K
Sbjct: 19 PETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDALKAK 70
>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 = 72.8 bits (177), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 91/177 (51%), Gaps = 17/177 (9%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
V++ ++ + + FA FG + S ++ DS + KG+ FV++E EAAQ A++ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 177 NGMLINDKQVYVG----------LFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKI 226
N +++ + + VG + + E A+ F +YV ++ + ++D+D+K +
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEAR-----AFNRIYVASVHQDLSDDDIKSV 130
Query: 227 FGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTNNDKVWYVGRA 282
F FG I S + +D + GK + +GF+ ++ ++ AV +N + VG+A
Sbjct: 131 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 68.9 bits (167), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 40/170 (23%), Positives = 83/170 (48%), Gaps = 10/170 (5%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
+YVG + + E + F+ + S+ + D G+A+V Y P+ A A E +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 90 NFMPINGKPIRI----MYSHRDPSIRK-----SGYGNVFIKNLDTSIDNKALCDTFAAFG 140
N + + G+ I++ P I + + +++ ++ + + + F AFG
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 141 TVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVG 189
+ SC +A D + G+ KGYGF+++E +++Q+A+ +N + + + VG
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 185
Score = 63.5 bits (153), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 47/179 (26%), Positives = 85/179 (47%), Gaps = 9/179 (5%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKL 267
VYV ++ + ++ +++ F FG I S + DS K + F FV ++ P+AA A+E++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 268 NGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKLK 327
N + VGR + + + E+ R +Y+ ++ ++D+ +K
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN-------RIYVASVHQDLSDDDIK 128
Query: 328 ELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVA 385
+F FG I SC + D G KG GF + + + A++ MN +G + L V A
Sbjct: 129 SVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 46/161 (28%), Positives = 74/161 (45%), Gaps = 29/161 (18%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKL 267
++V NL +T+ED K++F +G + + +D R FGF+ +S A A +L
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 268 NGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKLK 327
+GT + LR +F GA L +KNL +++E L+
Sbjct: 79 DGTILKSR---------------PLRIRF---------ATHGAALTVKNLSPVVSNELLE 114
Query: 328 ELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALN 368
+ FS+FG + V+VD G + G GF F+ A +AL
Sbjct: 115 QAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Score = 62.4 bits (150), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 14/145 (9%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+VG+L ++ E LF + + V + RD+ G+ ++ + A AK L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAI 149
+ + +P+RI ++ ++ +KNL + N+ L F+ FG V V +
Sbjct: 79 DGTILKSRPLRIRFATHGAALT--------VKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130
Query: 150 DSNGQSKGYGFVQFENEEAAQNAIK 174
D G++ G GFV+F + A+ A++
Sbjct: 131 DDRGRATGKGFVEFAAKPPARKALE 155
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 37/150 (24%), Positives = 71/150 (47%), Gaps = 17/150 (11%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
+F+ NL T I + F +G +V I+ + +G+GF++ E+ A+ A L
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGE--PSEVFINRD---RGFGFIRLESRTLAEIAKAEL 78
Query: 177 NGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSA 236
+G ++ + + + + + V NL+ V++E L++ F FG + A
Sbjct: 79 DGTILKSRPLRI------------RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKA 126
Query: 237 IVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
+V+ D G++ GFV F + A A+E+
Sbjct: 127 VVVVDDRGRATGKGFVEFAAKPPARKALER 156
>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 = 69.7 bits (169), Expect = 5e-12, Method: Composition-based stats.
Identities = 48/143 (33%), Positives = 77/143 (53%), Gaps = 18/143 (12%)
Query: 122 NLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIK---MLN 177
N DT+ DN L + F +GTV K+ D + G+S+G+GF+ FE + +K +L+
Sbjct: 12 NWDTTEDN--LREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILD 69
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAI 237
G +I+ K R R +Q+ + K ++V + V ++ ++ F +GTI A
Sbjct: 70 GKVIDPK--------RAIPRDEQDKTGK---IFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 238 VMKDSD-GKSRCFGFVNFQSPDA 259
+M D D G+SR FGFV + S DA
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADA 141
Score = 64.3 bits (155), Expect = 2e-10, Method: Composition-based stats.
Identities = 39/159 (24%), Positives = 78/159 (49%), Gaps = 22/159 (13%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKL 267
+++ L T+++L++ FG +GT+T +MKD + G+SR FGF++F+ P + V
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV--- 62
Query: 268 NGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKLK 327
+ + D + + I R E+ K +++ + + ++ +
Sbjct: 63 -----------------KTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFE 105
Query: 328 ELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATR 365
E FS++GTI ++M+D+ G S+G GF + + R
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
Score = 54.7 bits (130), Expect = 2e-07, Method: Composition-based stats.
Identities = 30/143 (20%), Positives = 71/143 (49%), Gaps = 11/143 (7%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
+++G L + E L + F + V +++ +D + S G+ ++++ P +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 90 NFMPINGK---PIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCK 146
+ + +GK P R + P + G +F+ + + K + F+ +GT++ +
Sbjct: 66 HIL--DGKVIDPKRAI-----PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 147 VAIDSN-GQSKGYGFVQFENEEA 168
+ +D + GQS+G+GFV +++ +A
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADA 141
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 4/71 (5%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMP---EEATRAL 367
+++ L+ ++ L+E F ++GT+T K+M D G S+G GF +F P +E +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 368 NEMNGKMIGRK 378
+ ++GK+I K
Sbjct: 66 HILDGKVIDPK 76
>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
Binding Protein
Length = 144
Score = 69.3 bits (168), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 44/52 (84%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P ++ +MLGE+L+PL++ + P A K+TGMLLE+D +E+LH++ESPE+L++K
Sbjct: 63 PQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 114
>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 = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 44/52 (84%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P ++ +MLGE+L+PL++ + P A K+TGMLLE+D +E+LH++ESPE+L++K
Sbjct: 17 PQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 68
>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 = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 87/177 (49%), Gaps = 17/177 (9%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
V++ ++ + + FA FG + S + DS + KG+ FV++E EAAQ A++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 177 NGMLINDKQVYVG----------LFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKI 226
N + + + + VG + + E A+ F +YV ++ + ++D+D+K +
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEAR-----AFNRIYVASVHQDLSDDDIKSV 129
Query: 227 FGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTNNDKVWYVGRA 282
F FG I S + +D + GK + +GF+ ++ ++ AV N + VG+A
Sbjct: 130 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 66.2 bits (160), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 40/170 (23%), Positives = 80/170 (47%), Gaps = 10/170 (5%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
+YVG + + E + F+ + S+ D G+A+V Y P+ A A E
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 90 NFMPINGKPIRI----MYSHRDPSIRK-----SGYGNVFIKNLDTSIDNKALCDTFAAFG 140
N + + G+ I++ P I + + +++ ++ + + + F AFG
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 141 TVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVG 189
+ SC +A D + G+ KGYGF+++E +++Q+A+ N + + + VG
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVG 184
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 46/179 (25%), Positives = 82/179 (45%), Gaps = 9/179 (5%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKL 267
VYV ++ + ++ +++ F FG I S DS K + F FV ++ P+AA A+E+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 268 NGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKLK 327
N + VGR + + + E+ R +Y+ ++ ++D+ +K
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN-------RIYVASVHQDLSDDDIK 127
Query: 328 ELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVA 385
+F FG I SC + D G KG GF + + + A++ N +G + L V A
Sbjct: 128 SVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
>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 = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 44/52 (84%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P ++ +MLGE+L+PL++ + P A K+TGMLLE+D +E+LH++ESPE+L++K
Sbjct: 17 PQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 68
>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 = 68.2 bits (165), Expect = 1e-11, Method: Composition-based stats.
Identities = 27/52 (51%), Positives = 44/52 (84%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P ++ +MLGE+L+PL++ + P A K+TGMLLE+D +E+LH++ESPE+L++K
Sbjct: 17 PQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 68
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
Score = 68.2 bits (165), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 44/52 (84%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P ++ +MLGE+L+PL++ + P A K+TGMLLE+D +E+LH++ESPE+L++K
Sbjct: 15 PQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 66
>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 = 68.2 bits (165), Expect = 1e-11, Method: Composition-based stats.
Identities = 27/52 (51%), Positives = 44/52 (84%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P ++ +MLGE+L+PL++ + P A K+TGMLLE+D +E+LH++ESPE+L++K
Sbjct: 16 PQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 67
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 67.8 bits (164), Expect = 2e-11, Method: Composition-based stats.
Identities = 27/52 (51%), Positives = 44/52 (84%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P ++ +MLGE+L+PL++ + P A K+TGMLLE+D +E+LH++ESPE+L++K
Sbjct: 16 PQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSK 67
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 67.4 bits (163), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 38/144 (26%), Positives = 71/144 (49%), Gaps = 14/144 (9%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+VG+L ++ E ++ LF + + V + +D+ G+ ++ A AK L
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVEL 78
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAI 149
+ MP+ GK +R+ ++ S+ ++NL + N+ L + F+ FG V V +
Sbjct: 79 DNMPLRGKQLRVRFACHSASLT--------VRNLPQYVSNELLEEAFSVFGQVERAVVIV 130
Query: 150 DSNGQSKGYGFVQFENEEAAQNAI 173
D G+ G G V+F + AA+ A+
Sbjct: 131 DDRGRPSGKGIVEFSGKPAARKAL 154
Score = 58.9 bits (141), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 42/162 (25%), Positives = 71/162 (43%), Gaps = 29/162 (17%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
+ ++V NL +T+E+++K+F +G + KD + FGF+ ++ A A +
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVE 77
Query: 267 LNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKL 326
L+ K LR +F A+L ++NL +++E L
Sbjct: 78 LDNMPLRGK---------------QLRVRF---------ACHSASLTVRNLPQYVSNELL 113
Query: 327 KELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALN 368
+E FS FG + V+VD G G G FS A +AL+
Sbjct: 114 EEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALD 155
Score = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 38/151 (25%), Positives = 67/151 (44%), Gaps = 17/151 (11%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+F+ NL I + + F +G + D KG+GF++ E A+ A L+
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 79
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAI 237
M + KQ+ V + ++ V NL + V++E L++ F FG + A+
Sbjct: 80 NMPLRGKQLRV------------RFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAV 127
Query: 238 VMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
V+ D G+ G V F AA A+++ +
Sbjct: 128 VIVDDRGRPSGKGIVEFSGKPAARKALDRCS 158
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 60.5 bits (145), Expect = 3e-09, Method: Composition-based stats.
Identities = 33/88 (37%), Positives = 51/88 (57%), Gaps = 2/88 (2%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSC-KVAIDSN-GQSKGYGFVQFENEEAAQ 170
SG +FI NLD ID K L DTF+AFG +L K+ D + G SKGY F+ F + +A+
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 171 NAIKMLNGMLINDKQVYVGLFVRRQERA 198
AI+ +NG + ++ + V ++ +
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSKG 90
Score = 48.9 bits (115), Expect = 8e-06, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 49/85 (57%), Gaps = 1/85 (1%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSV-RVCRDQSKRSSLGYAYVNYSNPQDAAN 84
G+ +++G+L+ ++E LYD FS ++ ++ RD +S GYA++N+++ +
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 85 AKEALNFMPINGKPIRIMYSHRDPS 109
A EA+N + +PI + Y+ + S
Sbjct: 64 AIEAMNGQYLCNRPITVSYAFKKDS 88
Score = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 49/84 (58%), Gaps = 2/84 (2%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTI-TSCKVMVD-QHGFSKGSGFAAFSMPEEATRAL 367
+ +++ NLD I+++ L + FS FG I + K+M D G SKG F F+ + + A+
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 368 NEMNGKMIGRKPLYVAVAQRKEER 391
MNG+ + +P+ V+ A +K+ +
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSK 89
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTI-TSAIVMKDSD-GKSRCFGFVNFQSPDAAAAAV 264
+ +++ NL + ++ L F FG I + +M+D D G S+ + F+NF S DA+ AA+
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 265 EKLNG 269
E +NG
Sbjct: 66 EAMNG 70
>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 = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 51/93 (54%), Gaps = 1/93 (1%)
Query: 302 SRYEKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMP 360
S+ E +GANL++ +L D+ L ++F FG + S KV +D Q SK GF ++ P
Sbjct: 18 SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77
Query: 361 EEATRALNEMNGKMIGRKPLYVAVAQRKEERKA 393
A A+ MNG IG K L V + + K + K+
Sbjct: 78 VSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 44/71 (61%), Gaps = 1/71 (1%)
Query: 200 QNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSPD 258
Q P+ N+++ +L + D+DL ++F FG + SA V D S+CFGFV++ +P
Sbjct: 19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
Query: 259 AAAAAVEKLNG 269
+A AA++ +NG
Sbjct: 79 SAQAAIQSMNG 89
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQFENEEAAQNAIKM 175
N+FI +L ++ L F FG V+S KV ID SK +GFV ++N +AQ AI+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 176 LNGMLINDKQVYVGL 190
+NG I K++ V L
Sbjct: 87 MNGFQIGMKRLKVQL 101
Score = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++ L Q + L +F VVS +V D+ S + +V+Y NP A A +++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSG 114
N I K +++ R + KSG
Sbjct: 88 NGFQIGMKRLKVQL-KRSKNDSKSG 111
>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 = 59.3 bits (142), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 46/81 (56%)
Query: 24 GYGNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAA 83
G G +L V L QN+ + +L LFS + +V S ++ RD+ SLGY +VNY +DA
Sbjct: 1 GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 84 NAKEALNFMPINGKPIRIMYS 104
A LN + + K I++ Y+
Sbjct: 61 RAINTLNGLRLQSKTIKVSYA 81
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 204 PKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAA 262
P TN+ VN L + +T ++L+ +F G + SA +++D G S +GFVN+ + A
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 263 AVEKLNGTTNNDKVWYVGRAQ 283
A+ LNG K V A+
Sbjct: 62 AINTLNGLRLQSKTIKVSYAR 82
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALN 368
NL + L ++ ++L+ LFS G + S K++ D+ G S G GF + ++A RA+N
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 369 EMNGKMIGRKPLYVAVAQ 386
+NG + K + V+ A+
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 114 GYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNA 172
G N+ + L ++ L F++ G V S K+ D G S GYGFV + + A+ A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 173 IKMLNGMLINDKQVYV 188
I LNG+ + K + V
Sbjct: 63 INTLNGLRLQSKTIKV 78
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/160 (26%), Positives = 73/160 (45%), Gaps = 16/160 (10%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKR--SSLGYAYVNYSNPQDAANA 85
+ ++VG + + +E L +LF Q V + V RD+S+ S G +V + + A A
Sbjct: 16 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 75
Query: 86 KEALNFM--------PINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFA 137
+ AL+ M PI KP S ++ ++ +FI + + F+
Sbjct: 76 QNALHNMKVLPGMHHPIQMKPAD---SEKNNAVEDR---KLFIGMISKKCTENDIRVMFS 129
Query: 138 AFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+FG + C++ +G S+G FV F AQ AIK ++
Sbjct: 130 SFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 39/157 (24%), Positives = 74/157 (47%), Gaps = 11/157 (7%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNG---QSKGYGFVQFENEEAAQNAIK 174
+F+ + + K L + F +G V V D + QSKG FV F +AA A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 175 MLNGMLINDKQVYVGLFVRRQER---AQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFG 231
L+ M +V G+ Q + +++N + + +++ +++ T+ D++ +F FG
Sbjct: 78 ALHNM-----KVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 132
Query: 232 TITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
I +++ DG SR FV F + A A++ ++
Sbjct: 133 QIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 81/183 (44%), Gaps = 20/183 (10%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG---KSRCFGFVNFQSPDAAAAAVE 265
++V + T +++DL+++F +G + V++D +S+ FV F + AA A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
L+ N KV G + AD E+ + E K L++ + +
Sbjct: 78 ALH----NMKV-LPGMHHPIQMKPAD------SEKNNAVEDRK---LFIGMISKKCTEND 123
Query: 326 LKELFSEFGTITSCKVMVDQHGFSKGSGFAAFS---MPEEATRALNEMNGKMIGRKPLYV 382
++ +FS FG I C+++ G S+G F F+ M + A +A+++ P+ V
Sbjct: 124 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 183
Query: 383 AVA 385
A
Sbjct: 184 KFA 186
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 42/160 (26%), Positives = 73/160 (45%), Gaps = 16/160 (10%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKR--SSLGYAYVNYSNPQDAANA 85
+ ++VG + + +E L +LF Q V + V RD+S+ S G +V + + A A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 86 KEALNFM--------PINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFA 137
+ AL+ M PI KP S ++ ++ +FI + + F+
Sbjct: 64 QNALHNMKVLPGMHHPIQMKPAD---SEKNNAVEDR---KLFIGMISKKCTENDIRVMFS 117
Query: 138 AFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+FG + C++ +G S+G FV F AQ AIK ++
Sbjct: 118 SFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 39/157 (24%), Positives = 74/157 (47%), Gaps = 11/157 (7%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNG---QSKGYGFVQFENEEAAQNAIK 174
+F+ + + K L + F +G V V D + QSKG FV F +AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 175 MLNGMLINDKQVYVGLFVRRQER---AQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFG 231
L+ M +V G+ Q + +++N + + +++ +++ T+ D++ +F FG
Sbjct: 66 ALHNM-----KVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 120
Query: 232 TITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
I +++ DG SR FV F + A A++ ++
Sbjct: 121 QIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 81/183 (44%), Gaps = 20/183 (10%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG---KSRCFGFVNFQSPDAAAAAVE 265
++V + T +++DL+++F +G + V++D +S+ FV F + AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 266 KLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEK 325
L+ N KV G + AD E+ + E K L++ + +
Sbjct: 66 ALH----NMKV-LPGMHHPIQMKPAD------SEKNNAVEDRK---LFIGMISKKCTEND 111
Query: 326 LKELFSEFGTITSCKVMVDQHGFSKGSGFAAFS---MPEEATRALNEMNGKMIGRKPLYV 382
++ +FS FG I C+++ G S+G F F+ M + A +A+++ P+ V
Sbjct: 112 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171
Query: 383 AVA 385
A
Sbjct: 172 KFA 174
>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 = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/52 (46%), Positives = 39/52 (75%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P + + LGE+L+PL++ P A K+TG LLE+D +E+L+ +ESPE+L++K
Sbjct: 17 PQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLESPESLRSK 68
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 1/85 (1%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKE 87
+L V L QN+ + + LF + + S ++ RD+ SLGY +VNYS+P DA A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 88 ALNFMPINGKPIRIMYSH-RDPSIR 111
LN + + K I++ Y+ SIR
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASIR 89
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVE 265
TN+ VN L + +T ++ K +FG G I S +++D G+S +GFVN+ P+ A A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 266 KLNGTTNNDKVWYVGRAQ 283
LNG K V A+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALN 368
NL + L ++ ++ K LF G I SCK++ D+ G S G GF +S P +A +A+N
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 369 EMNGKMIGRKPLYVAVAQ 386
+NG + K + V+ A+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 136 FAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
F + G + SCK+ D GQS GYGFV + + A AI LNG+ + K + V
Sbjct: 25 FGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKV 78
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 44/162 (27%), Positives = 72/162 (44%), Gaps = 11/162 (6%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQF---ENEEAAQNA 172
+FI L +++L F +GT+ C V D N + S+G+GFV + E +AA NA
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 173 I-KMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFG 231
++G ++ K+ V R++ + ++V + E + L+ F +G
Sbjct: 76 RPHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 130
Query: 232 TITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
I +M D GK R F FV F D+ V + T N
Sbjct: 131 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN 172
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 47/164 (28%), Positives = 77/164 (46%), Gaps = 31/164 (18%)
Query: 203 SPK----FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSP 257
SPK +++ L+ TDE L+ F +GT+T +VM+D + K SR FGFV +
Sbjct: 7 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY--- 63
Query: 258 DAAAAAVEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLK-GANLYLKN 316
A VE+++ N R K D R + +SR + + GA+L +K
Sbjct: 64 ----ATVEEVDAAMN-------ARPHK-----VDGRVVEPKRAVSREDSQRPGAHLTVKK 107
Query: 317 -----LDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFA 355
+ + + L++ F ++G I ++M D+ G K GFA
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFA 150
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 40/185 (21%), Positives = 81/185 (43%), Gaps = 15/185 (8%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++G L + L F Q + V RD + + S G+ +V Y+ ++ A+
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE---VDAAM 73
Query: 90 NFMP--INGK---PIRIMYSHRDPSIRKSGY---GNVFIKNLDTSIDNKALCDTFAAFGT 141
N P ++G+ P R + R+ S R + +F+ + + L D F +G
Sbjct: 74 NARPHKVDGRVVEPKRAVS--REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 131
Query: 142 VLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQ 200
+ ++ D +G+ +G+ FV F++ ++ + I + +N V + +QE A
Sbjct: 132 IEVIEIMTDRGSGKKRGFAFVTFDDHDSV-DKIVIQKYHTVNGHNCEVRKALSKQEMASA 190
Query: 201 NVSPK 205
+ S +
Sbjct: 191 SSSQR 195
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG-FSKGSGFAAFSMPEEATRALNE 369
L++ L DE L+ F ++GT+T C VM D + S+G GF ++ EE A+N
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 370 MNGKMIGR 377
K+ GR
Sbjct: 76 RPHKVDGR 83
>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 = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 44/162 (27%), Positives = 72/162 (44%), Gaps = 11/162 (6%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQF---ENEEAAQNA 172
+FI L +++L F +GT+ C V D N + S+G+GFV + E +AA NA
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 173 I-KMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFG 231
++G ++ K+ V R++ + ++V + E + L+ F +G
Sbjct: 75 RPHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 232 TITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
I +M D GK R F FV F D+ V + T N
Sbjct: 130 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN 171
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 47/164 (28%), Positives = 77/164 (46%), Gaps = 31/164 (18%)
Query: 203 SPK----FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSP 257
SPK +++ L+ TDE L+ F +GT+T +VM+D + K SR FGFV +
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY--- 62
Query: 258 DAAAAAVEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLK-GANLYLKN 316
A VE+++ N R K D R + +SR + + GA+L +K
Sbjct: 63 ----ATVEEVDAAMN-------ARPHK-----VDGRVVEPKRAVSREDSQRPGAHLTVKK 106
Query: 317 -----LDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFA 355
+ + + L++ F ++G I ++M D+ G K GFA
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFA 149
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 33/153 (21%), Positives = 68/153 (44%), Gaps = 14/153 (9%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++G L + L F Q + V RD + + S G+ +V Y+ ++ A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE---VDAAM 72
Query: 90 NFMP--INGK---PIRIMYSHRDPSIRKSGY---GNVFIKNLDTSIDNKALCDTFAAFGT 141
N P ++G+ P R + R+ S R + +F+ + + L D F +G
Sbjct: 73 NARPHKVDGRVVEPKRAVS--REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 142 VLSCKVAID-SNGQSKGYGFVQFENEEAAQNAI 173
+ ++ D +G+ +G+ FV F++ ++ +
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG-FSKGSGFAAFSMPEEATRALNE 369
L++ L DE L+ F ++GT+T C VM D + S+G GF ++ EE A+N
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 370 MNGKMIGR 377
K+ GR
Sbjct: 75 RPHKVDGR 82
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
++VG ++++ E L D F Q ++ + + D+ G+A+V + + D+ +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 165
Query: 90 NFMPING 96
+ +NG
Sbjct: 166 KYHTVNG 172
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 56.2 bits (134), Expect = 5e-08, Method: Composition-based stats.
Identities = 32/75 (42%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQFENEEAAQNAIKM 175
N+FI +L + L TF FG V+S KV ID SK +GFV F+N ++AQ AIK
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 176 LNGMLINDKQVYVGL 190
+NG + K++ V L
Sbjct: 102 MNGFQVGTKRLKVQL 116
Score = 56.2 bits (134), Expect = 6e-08, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 198 AQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQS 256
+Q P+ N+++ +L + TD DL F FG + SA V D S+CFGFV+F +
Sbjct: 32 GKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDN 91
Query: 257 PDAAAAAVEKLNG 269
PD+A A++ +NG
Sbjct: 92 PDSAQVAIKAMNG 104
Score = 52.0 bits (123), Expect = 1e-06, Method: Composition-based stats.
Identities = 30/83 (36%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 305 EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEA 363
E +G NL++ +L D L F FG + S KV +D Q SK GF +F P+ A
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 364 TRALNEMNGKMIGRKPLYVAVAQ 386
A+ MNG +G K L V + +
Sbjct: 96 QVAIKAMNGFQVGTKRLKVQLKK 118
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 36/73 (49%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+L++ L Q ++ L F V+S +V D+ S + +V++ NP A A +A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 89 LNFMPINGKPIRI 101
+N + K +++
Sbjct: 102 MNGFQVGTKRLKV 114
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 48/79 (60%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALN 368
G+ +++ NLD + +KLKE+FS G + ++ D+ G S+G G F EA +A++
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 369 EMNGKMIGRKPLYVAVAQR 387
NG+++ +P++V + +R
Sbjct: 75 MFNGQLLFDRPMHVKMDER 93
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
VF+ NLD + K L + F+ G V+ + D +G+S+G G V FE A AI M
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 177 NGMLINDKQVYVGLFVRRQERA 198
NG L+ D+ ++ V+ ERA
Sbjct: 77 NGQLLFDRPMH----VKMDERA 94
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 31/94 (32%), Positives = 47/94 (50%), Gaps = 4/94 (4%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
+ V+V NL V + LK++F G + A +++D DGKSR G V F+ A A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 267 LNGTTNNDKVWYVGRAQKRAEREADLRAKFEQER 300
NG D+ +V + +RA + D F ER
Sbjct: 76 FNGQLLFDRPMHV-KMDERALPKGDF---FPPER 105
>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 = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKM 175
+VF+ +L I + + FA FG + +V D + G+SKGYGFV F N+ A+NAI+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 176 LNGMLINDKQVYVGLFVRR 194
+ G + +Q+ R+
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
++VGDL + + F+ ++ RV +D + S GY +V++ N DA NA + +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSGY 115
+ G+ IR ++ R P KS Y
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPKSTY 103
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEK 266
+V+V +L+ +T ED+K F FG I+ A V+KD + GKS+ +GFV+F + A A+++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 267 LNG 269
+ G
Sbjct: 77 MGG 79
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNE 369
++++ +L I E +K F+ FG I+ +V+ D G SKG GF +F +A A+ +
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 370 MNGKMIGRKPLYVAVAQRK 388
M G+ +G + + A RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
>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 = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 46/78 (58%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+L+VGDL NV++ L + F +S V D SS GY +V++++ DA NA ++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 89 LNFMPINGKPIRIMYSHR 106
+ +NG+P+RI ++ +
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNE 369
NL++ +L+ +++DE L+ F +F + S VM D Q G S+G GF +F+ ++A A++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 370 MNGKMIGRKPLYVAVAQRKEE 390
M G+ + +PL + A + E
Sbjct: 63 MQGQDLNGRPLRINWAAKLEH 83
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 42/67 (62%), Gaps = 1/67 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKM 175
N+F+ +L+ ++D++ L + F F + LS V D G S+GYGFV F +++ AQNA+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 176 LNGMLIN 182
+ G +N
Sbjct: 63 MQGQDLN 69
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEK 266
N++V +L V DE L+ F F + S VM D G SR +GFV+F S D A A++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 267 LNG 269
+ G
Sbjct: 63 MQG 65
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 55.5 bits (132), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 43/77 (55%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKE 87
+L V L QN + +L LFS + +V S ++ RD+ SLGY +VNY +DA A
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 88 ALNFMPINGKPIRIMYS 104
LN + + K I++ Y+
Sbjct: 80 TLNGLRLQSKTIKVSYA 96
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 307 LKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATR 365
+G NL + L + ++L+ LFS G + S K++ D+ G S G GF + ++A R
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 366 ALNEMNGKMIGRKPLYVAVAQ 386
A+N +NG + K + V+ A+
Sbjct: 77 AINTLNGLRLQSKTIKVSYAR 97
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 200 QNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPD 258
+N+ + TN+ VN L + T ++L+ +F G + SA +++D G S +GFVN+ +
Sbjct: 13 ENLYFQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAK 72
Query: 259 AAAAAVEKLNGTTNNDKVWYVGRAQ 283
A A+ LNG K V A+
Sbjct: 73 DAERAINTLNGLRLQSKTIKVSYAR 97
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKM 175
N+ + L + L F++ G V S K+ D G S GYGFV + + A+ AI
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 176 LNGMLINDKQVYV 188
LNG+ + K + V
Sbjct: 81 LNGLRLQSKTIKV 93
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+VG L + NE L +FS+ Q+ V V +D+ + S G+ +V + N DA +A A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 90 NFMPINGKPIRI 101
N ++G+ IR+
Sbjct: 75 NGKSVDGRQIRV 86
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG-KSRCFGFVNFQSPDAAAAAVEKL 267
++V L+ ++ L+++F +G I+ +V+KD + +SR FGFV F++ D A A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 268 NGTTNNDKVWYVGRAQKRAE 287
NG + + + V +A K ++
Sbjct: 75 NGKSVDGRQIRVDQAGKSSD 94
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQFENEEAAQN 171
S G +F+ L + ++L F+ +G + V D Q S+G+GFV FEN + A++
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 172 AIKMLNGMLINDKQVYV 188
A+ +NG ++ +Q+ V
Sbjct: 70 AMMAMNGKSVDGRQIRV 86
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG-FSKGSGFAAFSMPEEATRALNEM 370
L++ L N++ L+++FS++G I+ V+ D+ S+G GF F ++A A+ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 371 NGKMIGRKPLYVAVAQRKEERKA 393
NGK + + + V A + + ++
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRS 97
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 49/90 (54%)
Query: 290 ADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFS 349
+ L+A Q ++++ ++ NLY+ NL S+++++L+ + FG + S +++ D G S
Sbjct: 6 SGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTS 65
Query: 350 KGSGFAAFSMPEEATRALNEMNGKMIGRKP 379
+G GFA E+ + NGK I P
Sbjct: 66 RGVGFARMESTEKCEAVIGHFNGKFIKTPP 95
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 37/65 (56%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
N++I NL S+D + L + FG V+S ++ DS+G S+G GF + E+ E + I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 177 NGMLI 181
NG I
Sbjct: 87 NGKFI 91
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 192 VRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGF 251
V+ Q QQ P TN+Y++NL ++ +++L+ + FG + S +++DS G SR GF
Sbjct: 13 VQAQMAKQQEQDP--TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGF 70
Query: 252 VNFQSPDAAAAAVEKLNG 269
+S + A + NG
Sbjct: 71 ARMESTEKCEAVIGHFNG 88
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRS-SLGYAYVNYSNPQDA 82
+LY+ +L +++E +L ++ QV+S R+ RD S S +G+A + + +A
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 81
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 54.3 bits (129), Expect = 2e-07, Method: Composition-based stats.
Identities = 29/76 (38%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNA 172
SG +F++NL K L D F G VL + ++ NG+SKG G V+FE+ E A+ A
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 61
Query: 173 IKMLNGMLINDKQVYV 188
+M+NGM ++ +++ V
Sbjct: 62 CRMMNGMKLSGREIDV 77
Score = 38.5 bits (88), Expect = 0.013, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNE 369
+ ++++NL + LK+ F+E G + + + ++G SKG G F PE A RA
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVAERACRM 64
Query: 370 MNG-KMIGRK 378
MNG K+ GR+
Sbjct: 65 MNGMKLSGRE 74
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
+ ++V NL T + LK F G + A + K +GKS+ G V F+SP+ A A
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRM 64
Query: 267 LNG 269
+NG
Sbjct: 65 MNG 67
>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 = 53.9 bits (128), Expect = 2e-07, Method: Composition-based stats.
Identities = 44/161 (27%), Positives = 72/161 (44%), Gaps = 11/161 (6%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQF---ENEEAAQNA- 172
+FI L +++L F +GT+ C V D N + S+G+GFV + E +AA NA
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 173 IKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGT 232
++G ++ K+ V R++ + ++V + E + L+ F +G
Sbjct: 69 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 123
Query: 233 ITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
I +M D GK R F FV F D+ V + T N
Sbjct: 124 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN 164
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 43/157 (27%), Positives = 73/157 (46%), Gaps = 25/157 (15%)
Query: 205 KFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSPDAAAAA 263
+ +++ L+ TDE L+ F +GT+T +VM+D + K SR FGFV + A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-------AT 57
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKN-----LD 318
VE+++ N R K R + + +E R GA+L +K +
Sbjct: 58 VEEVDAAMN-------ARPHKVDGRVVEPKRAVSREDSQR----PGAHLTVKKIFVGGIK 106
Query: 319 DSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFA 355
+ + L++ F ++G I ++M D+ G K GFA
Sbjct: 107 EDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFA 142
Score = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 31/151 (20%), Positives = 67/151 (44%), Gaps = 10/151 (6%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++G L + L F Q + V RD + + S G+ +V Y+ ++ A+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE---VDAAM 65
Query: 90 NFMP--INGKPIRIMYS-HRDPSIRKSGY---GNVFIKNLDTSIDNKALCDTFAAFGTVL 143
N P ++G+ + + R+ S R + +F+ + + L D F +G +
Sbjct: 66 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125
Query: 144 SCKVAID-SNGQSKGYGFVQFENEEAAQNAI 173
++ D +G+ +G+ FV F++ ++ +
Sbjct: 126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNEM 370
L++ L DE L+ F ++GT+T C VM D + S+G GF ++ EE A+N
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 371 NGKMIGR 377
K+ GR
Sbjct: 69 PHKVDGR 75
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
++VG ++++ E L D F Q ++ + + D+ G+A+V + + D+ +
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 158
Query: 90 NFMPING 96
+ +NG
Sbjct: 159 KYHTVNG 165
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSD-GKSRCFGFVNFQSPDAAAAAVE 265
+ +YV +L +T++ L+ IF FG I + ++MKDSD G+S+ +GF+ F + A A+E
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 266 KLNGTTNNDKVWYVGRAQKRAE 287
+LNG + VG +R +
Sbjct: 66 QLNGFELAGRPMRVGHVTERLD 87
Score = 48.9 bits (115), Expect = 9e-06, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G+ LYVG L N+ E L +F ++ ++ + +D S GY ++ +S+ + A A
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 86 KEALNFMPINGKPIRI 101
E LN + G+P+R+
Sbjct: 64 LEQLNGFELAGRPMRV 79
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALN 368
+ LY+ +L +I ++ L+ +F FG I + +M D G SKG GF FS E A RAL
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 369 EMNGKMIGRKPLYVA 383
++NG + +P+ V
Sbjct: 66 QLNGFELAGRPMRVG 80
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSN-GQSKGYGFVQFENEEAAQN 171
SG +++ +L +I L F FG + + + DS+ G+SKGYGF+ F + E A+
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 172 AIKMLNGMLINDKQVYVGLFVRR 194
A++ LNG + + + VG R
Sbjct: 63 ALEQLNGFELAGRPMRVGHVTER 85
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 44/161 (27%), Positives = 72/161 (44%), Gaps = 11/161 (6%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQF---ENEEAAQNA- 172
+FI L +++L F +GT+ C V D N + S+G+GFV + E +AA NA
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 173 IKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGT 232
++G ++ K+ V R++ + ++V + E + L+ F +G
Sbjct: 76 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 233 ITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
I +M D GK R F FV F D+ V + T N
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN 171
Score = 53.5 bits (127), Expect = 3e-07, Method: Composition-based stats.
Identities = 46/163 (28%), Positives = 75/163 (46%), Gaps = 29/163 (17%)
Query: 203 SPK----FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSP 257
SPK +++ L+ TDE L+ F +GT+T +VM+D + K SR FGFV +
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY--- 62
Query: 258 DAAAAAVEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKN- 316
A VE+++ N R K R + + +E R GA+L +K
Sbjct: 63 ----ATVEEVDAAMN-------ARPHKVDGRVVEPKRAVSREDSQR----PGAHLTVKKI 107
Query: 317 ----LDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFA 355
+ + + L++ F ++G I ++M D+ G K GFA
Sbjct: 108 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFA 149
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 31/151 (20%), Positives = 67/151 (44%), Gaps = 10/151 (6%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++G L + L F Q + V RD + + S G+ +V Y+ ++ A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE---VDAAM 72
Query: 90 NFMP--INGKPIRIMYS-HRDPSIRKSGY---GNVFIKNLDTSIDNKALCDTFAAFGTVL 143
N P ++G+ + + R+ S R + +F+ + + L D F +G +
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 144 SCKVAID-SNGQSKGYGFVQFENEEAAQNAI 173
++ D +G+ +G+ FV F++ ++ +
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNEM 370
L++ L DE L+ F ++GT+T C VM D + S+G GF ++ EE A+N
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 371 NGKMIGR 377
K+ GR
Sbjct: 76 PHKVDGR 82
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
++VG ++++ E L D F Q ++ + + D+ G+A+V + + D+ +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 165
Query: 90 NFMPING 96
+ +NG
Sbjct: 166 KYHTVNG 172
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 44/161 (27%), Positives = 72/161 (44%), Gaps = 11/161 (6%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQF---ENEEAAQNA- 172
+FI L +++L F +GT+ C V D N + S+G+GFV + E +AA NA
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 173 IKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGT 232
++G ++ K+ V R++ + ++V + E + L+ F +G
Sbjct: 74 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 128
Query: 233 ITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
I +M D GK R F FV F D+ V + T N
Sbjct: 129 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN 169
Score = 53.5 bits (127), Expect = 3e-07, Method: Composition-based stats.
Identities = 46/163 (28%), Positives = 75/163 (46%), Gaps = 29/163 (17%)
Query: 203 SPK----FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSP 257
SPK +++ L+ TDE L+ F +GT+T +VM+D + K SR FGFV +
Sbjct: 4 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY--- 60
Query: 258 DAAAAAVEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKN- 316
A VE+++ N R K R + + +E R GA+L +K
Sbjct: 61 ----ATVEEVDAAMN-------ARPHKVDGRVVEPKRAVSREDSQR----PGAHLTVKKI 105
Query: 317 ----LDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFA 355
+ + + L++ F ++G I ++M D+ G K GFA
Sbjct: 106 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFA 147
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 31/151 (20%), Positives = 67/151 (44%), Gaps = 10/151 (6%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++G L + L F Q + V RD + + S G+ +V Y+ ++ A+
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE---VDAAM 70
Query: 90 NFMP--INGKPIRIMYS-HRDPSIRKSGY---GNVFIKNLDTSIDNKALCDTFAAFGTVL 143
N P ++G+ + + R+ S R + +F+ + + L D F +G +
Sbjct: 71 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 130
Query: 144 SCKVAID-SNGQSKGYGFVQFENEEAAQNAI 173
++ D +G+ +G+ FV F++ ++ +
Sbjct: 131 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNEM 370
L++ L DE L+ F ++GT+T C VM D + S+G GF ++ EE A+N
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 371 NGKMIGR 377
K+ GR
Sbjct: 74 PHKVDGR 80
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
++VG ++++ E L D F Q ++ + + D+ G+A+V + + D+ +
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 163
Query: 90 NFMPING 96
+ +NG
Sbjct: 164 KYHTVNG 170
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 29/76 (38%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNA 172
SG +F++NL K L D F G VL + ++ NG+SKG G V+FE+ E A+ A
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 64
Query: 173 IKMLNGMLINDKQVYV 188
+M+NGM ++ +++ V
Sbjct: 65 CRMMNGMKLSGREIDV 80
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
++++NL + LK+ F+E G + + + ++G SKG G F PE A RA MN
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVAERACRMMN 69
Query: 372 G-KMIGRK 378
G K+ GR+
Sbjct: 70 GMKLSGRE 77
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
++V NL T + LK F G + A + K +GKS+ G V F+SP+ A A +N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMMN 69
Query: 269 G 269
G
Sbjct: 70 G 70
>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 = 29/82 (35%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKM 175
N+ + + T++D L F +G + S K+ D QS+GYGFV+F++ +AQ AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 176 LNGMLINDKQVYVGLFVRRQER 197
LNG I +K++ V L +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/93 (33%), Positives = 47/93 (50%), Gaps = 2/93 (2%)
Query: 198 AQQNVSPK-FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQ 255
Q N P N+ VN + TV + L+++F +G I S ++ D + + SR +GFV FQ
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92
Query: 256 SPDAAAAAVEKLNGTTNNDKVWYVGRAQKRAER 288
S +A A+ LNG +K V A +R
Sbjct: 93 SGSSAQQAIAGLNGFNILNKRLKVALAASGHQR 125
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGF-SKGSGFAAFSMPEEATRALNE 369
NL + + ++++ +L++LF +G I S K++ D+ S+G GF F A +A+
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 370 MNGKMIGRKPLYVAVAQRKEER 391
+NG I K L VA+A +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 46/75 (61%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
+ ++YVG L++ V+E L++LF Q VV+ + +D+ GY +V + + +DA A
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 87 EALNFMPINGKPIRI 101
+ ++ + + GKPIR+
Sbjct: 75 KIMDMIKLYGKPIRV 89
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKM 175
V++ LD + L + F G V++ + D GQ +GYGFV+F +EE A AIK+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 176 LNGMLINDKQVYV 188
++ + + K + V
Sbjct: 77 MDMIKLYGKPIRV 89
Score = 35.4 bits (80), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 305 EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEA 363
E+ + A +Y+ LD+ +++ L ELF + G + + + D+ G +G GF F E+A
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 364 TRALNEMNGKMIGRKPLYV 382
A+ M+ + KP+ V
Sbjct: 71 DYAIKIMDMIKLYGKPIRV 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 41/78 (52%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N L V L E L ++FS+ + V + DQ R S G+A+V + N DA AK
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 87 EALNFMPINGKPIRIMYS 104
E N M ++G+ IR+ +S
Sbjct: 106 ERANGMELDGRRIRVDFS 123
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 211 VNNLAETVTDEDLKKIFGHFGTITS-AIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
V L+ T+ DL+++F +G I +IV +SR F FV F++ D A A E+ NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Score = 36.6 bits (83), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQFENEEAAQNAIKML 176
VF +L T+ + L + F+ +G + + D + S+G+ FV FEN + A+ A +
Sbjct: 51 VFGLSLYTT--ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 177 NGMLINDKQVYVGLFVRRQ 195
NGM ++ +++ V + ++
Sbjct: 109 NGMELDGRRIRVDFSITKR 127
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG-FSKGSGFAAFSMPEEATRAL 367
G +LY D L+E+FS++G I ++ DQ S+G F F ++A A
Sbjct: 53 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 368 NEMNG-KMIGRK 378
NG ++ GR+
Sbjct: 106 ERANGMELDGRR 117
>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 = 53.5 bits (127), Expect = 4e-07, Method: Composition-based stats.
Identities = 41/157 (26%), Positives = 69/157 (43%), Gaps = 16/157 (10%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKR--SSLGYAYVNYSNPQDAANA 85
+ +VG + + +E L +LF Q V + V RD+S+ S G +V + + A A
Sbjct: 4 IKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 86 KEALN--------FMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFA 137
+ AL+ PI KP S ++ ++ +FI + + F+
Sbjct: 64 QNALHNXKVLPGXHHPIQXKPAD---SEKNNAVEDR---KLFIGXISKKCTENDIRVXFS 117
Query: 138 AFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIK 174
+FG + C++ +G S+G FV F AQ AIK
Sbjct: 118 SFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 38/153 (24%), Positives = 69/153 (45%), Gaps = 11/153 (7%)
Query: 119 FIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNG---QSKGYGFVQFENEEAAQNAIKM 175
F+ + + K L + F +G V V D + QSKG FV F +AA A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 176 LNGMLINDKQVYVGLFVRRQER---AQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGT 232
L+ + +V G Q + +++N + + +++ +++ T+ D++ F FG
Sbjct: 67 LH-----NXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ 121
Query: 233 ITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVE 265
I +++ DG SR FV F + A A++
Sbjct: 122 IEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 39/161 (24%), Positives = 70/161 (43%), Gaps = 17/161 (10%)
Query: 210 YVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG---KSRCFGFVNFQSPDAAAAAVEK 266
+V + T +++DL+++F +G + V++D +S+ FV F + AA A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 267 LNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKL 326
L+ N KV G + AD E+ + E K L++ + + +
Sbjct: 67 LH----NXKV-LPGXHHPIQXKPAD------SEKNNAVEDRK---LFIGXISKKCTENDI 112
Query: 327 KELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRAL 367
+ FS FG I C+++ G S+G F F+ A A+
Sbjct: 113 RVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 53.1 bits (126), Expect = 4e-07, Method: Composition-based stats.
Identities = 44/161 (27%), Positives = 72/161 (44%), Gaps = 11/161 (6%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQF---ENEEAAQNA- 172
+FI L +++L F +GT+ C V D N + S+G+GFV + E +AA NA
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 173 IKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGT 232
++G ++ K+ V R++ + ++V + E + L+ F +G
Sbjct: 75 PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 129
Query: 233 ITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
I +M D GK R F FV F D+ V + T N
Sbjct: 130 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVN 170
Score = 52.8 bits (125), Expect = 6e-07, Method: Composition-based stats.
Identities = 46/163 (28%), Positives = 75/163 (46%), Gaps = 29/163 (17%)
Query: 203 SPK----FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSP 257
SPK +++ L+ TDE L+ F +GT+T +VM+D + K SR FGFV +
Sbjct: 5 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY--- 61
Query: 258 DAAAAAVEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKN- 316
A VE+++ N R K R + + +E R GA+L +K
Sbjct: 62 ----ATVEEVDAAMN-------ARPHKVDGRVVEPKRAVSREDSQR----PGAHLTVKKI 106
Query: 317 ----LDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFA 355
+ + + L++ F ++G I ++M D+ G K GFA
Sbjct: 107 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFA 148
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 38/183 (20%), Positives = 80/183 (43%), Gaps = 11/183 (6%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++G L + L F Q + V RD + + S G+ +V Y+ ++ A+
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE---VDAAM 71
Query: 90 NFMP--INGKPIRIMYS-HRDPSIRKSGY---GNVFIKNLDTSIDNKALCDTFAAFGTVL 143
N P ++G+ + + R+ S R + +F+ + + L D F +G +
Sbjct: 72 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 131
Query: 144 SCKVAID-SNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQNV 202
++ D +G+ +G+ FV F++ ++ + I + +N V + +QE A +
Sbjct: 132 VIEIMTDRGSGKKRGFAFVTFDDHDSV-DKIVIQKYHTVNGHNCEVRKALSKQEMASASS 190
Query: 203 SPK 205
S +
Sbjct: 191 SQR 193
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNEM 370
L++ L DE L+ F ++GT+T C VM D + S+G GF ++ EE A+N
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 371 NGKMIGR 377
K+ GR
Sbjct: 75 PHKVDGR 81
>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma
Cruzi Poly(A)-Binding Protein
Length = 85
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 36/52 (69%)
Query: 558 PDDRTRMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
P+ + +LGE+LY + I P A+KVTGMLLEMD E+L+L+++P L K
Sbjct: 20 PEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAK 71
>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 = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 203 SPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAA 261
S K TN+YV NL T+TD+ L IFG +G+I +++D G+ R FV + + A
Sbjct: 10 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 69
Query: 262 AAVEKLN 268
A+ LN
Sbjct: 70 EAISALN 76
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 49/85 (57%), Gaps = 3/85 (3%)
Query: 305 EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEA 363
E +K NLY+ NL +I D++L +F ++G+I ++ D+ G +G F ++ EEA
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 364 TRALNEMNGKMI--GRKPLYVAVAQ 386
A++ +N + G +PL V +A+
Sbjct: 69 QEAISALNNVIPEGGSQPLSVRLAE 93
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 34/64 (53%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
+ +LYV +L + + + QL +F + +V + RD+ G A+V Y+ ++A A
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 87 EALN 90
ALN
Sbjct: 73 SALN 76
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 41/78 (52%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N L V L E L ++FS+ + V + DQ R S G+A+V + N DA AK
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 87 EALNFMPINGKPIRIMYS 104
E N M ++G+ IR+ +S
Sbjct: 72 ERANGMELDGRRIRVDFS 89
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 211 VNNLAETVTDEDLKKIFGHFGTITS-AIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
V L+ T+ DL+++F +G I +IV +SR F FV F++ D A A E+ NG
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Score = 36.6 bits (83), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 130 KALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
+ L + F+ +G + + D + S+G+ FV FEN + A+ A + NGM ++ +++ V
Sbjct: 27 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 86
Query: 189 GLFVRRQ 195
+ ++
Sbjct: 87 DFSITKR 93
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG-FSKGSGFAAFSMPEEATRAL 367
G +LY D L+E+FS++G I ++ DQ S+G F F ++A A
Sbjct: 19 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 368 NEMNG-KMIGRK 378
NG ++ GR+
Sbjct: 72 ERANGMELDGRR 83
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 41/78 (52%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N L V L E L ++FS+ + V + DQ R S G+A+V + N DA AK
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 87 EALNFMPINGKPIRIMYS 104
E N M ++G+ IR+ +S
Sbjct: 75 ERANGMELDGRRIRVDFS 92
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 211 VNNLAETVTDEDLKKIFGHFGTITS-AIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
V L+ T+ DL+++F +G I +IV +SR F FV F++ D A A E+ NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Score = 36.2 bits (82), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 130 KALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
+ L + F+ +G + + D + S+G+ FV FEN + A+ A + NGM ++ +++ V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Query: 189 GLFVRRQ 195
+ ++
Sbjct: 90 DFSITKR 96
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG-FSKGSGFAAFSMPEEATRAL 367
G +LY D L+E+FS++G I ++ DQ S+G F F ++A A
Sbjct: 22 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 368 NEMNG-KMIGRK 378
NG ++ GR+
Sbjct: 75 ERANGMELDGRR 86
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 49/85 (57%), Gaps = 2/85 (2%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++G L + NE L +F + + V + +D++ +S G+A++ + NP DA NA + +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSR-GFAFITFENPADAKNAAKDM 68
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSG 114
N ++GK I++ + + PS + G
Sbjct: 69 NGKSLHGKAIKVEQA-KKPSFQSGG 92
Score = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
+++ L ++ LK +FG G I+ +++KD KSR F F+ F++P A A + +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 269 GTTNNDKVWYVGRAQK 284
G + + K V +A+K
Sbjct: 70 GKSLHGKAIKVEQAKK 85
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%)
Query: 116 GNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKM 175
G +FI L+ + K L F G + + D +S+G+ F+ FEN A+NA K
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 176 LNGMLINDKQVYV 188
+NG ++ K + V
Sbjct: 68 MNGKSLHGKAIKV 80
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L++ L+ N++ LK +F + G I+ ++ D+ S+G F F P +A A +MN
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 372 GKMIGRKPLYVAVAQR 387
GK + K + V A++
Sbjct: 70 GKSLHGKAIKVEQAKK 85
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.4 bits (124), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSD-GKSRCFGFVNFQSPDAAAAAVEKL 267
+YV +L +T++ L+ IF FG I S +M DS+ G+S+ +GF+ F + A A+E+L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 268 NGTTNNDKVWYVGRAQKRAE 287
NG + VG +R +
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
Score = 52.0 bits (123), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G + LYVG L N+ E L +F ++ S+++ D S GY ++ +S+ + A A
Sbjct: 25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 86 KEALNFMPINGKPIRI 101
E LN + G+P+++
Sbjct: 85 LEQLNGFELAGRPMKV 100
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 49/80 (61%), Gaps = 2/80 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
LY+ +L +I ++ L+ +F FG I S ++M+D + G SKG GF FS E A +AL ++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 371 NGKMIGRKPLYVA-VAQRKE 389
NG + +P+ V V +R +
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+++ +L +I L F FG + S ++ +DS G+SKGYGF+ F + E A+ A++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 177 NGMLINDKQVYVGLFVRRQE 196
NG + + + VG R +
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
>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 = 52.0 bits (123), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
VF+ +D +D + FA +G+V K+ D G SKGYGFV F N+ Q ++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-- 68
Query: 177 NGMLINDKQVYVGLFVRRQERAQQNVSPK 205
+ + + K++ +G +R+Q + +V P+
Sbjct: 69 SQINFHGKKLKLGPAIRKQNLSTYHVQPR 97
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 32/52 (61%)
Query: 306 KLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAF 357
K+ +++ +D +++ +++ F+ +G++ K++ D+ G SKG GF +F
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 29/58 (50%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVE 265
V+V + + + +++ F +G++ ++ D G S+ +GFV+F + VE
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
>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 = 52.0 bits (123), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 59/275 (21%), Positives = 112/275 (40%), Gaps = 31/275 (11%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
V +KNL S + + F G ++ VA DS ++ + ++F + A AI +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTH 102
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAI 237
+ + ++ V ++ N + T +++ + + +I
Sbjct: 103 KV-VGQNEIIVSHLTE-------------CTLWXTNFPPSYTQRNIRDLLQDINVVALSI 148
Query: 238 VMKDSD-GKSRCFGFVNFQSPDAAAAAVEKLNGTTNNDKVWYVGRAQKRAEREADLRAKF 296
+ SR F +++ S + A VEKLNG K+ K +
Sbjct: 149 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL----KIEGYTLVTK-------VSNPL 197
Query: 297 EQERISRYEKLKGANLYLKNLDDSINDEK-LKELFSEFGTITSCKVMVDQ--HGFSKGSG 353
E+ + + L+G + ++NL + DE L+E F FG+I + Q H F+
Sbjct: 198 EKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCA 257
Query: 354 FAAFSMPEEATRALNEMNGKMIGRKPLYVAVAQRK 388
F F + A RAL + N ++G + + V++A +K
Sbjct: 258 FXVFENKDSAERAL-QXNRSLLGNREISVSLADKK 291
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 41/182 (22%), Positives = 87/182 (47%), Gaps = 17/182 (9%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKR--SSLGYAYVNYSN 78
+ S +L+ + + + + DL + VV++ + R S R +S +AY++ ++
Sbjct: 111 IVSHLTECTLWXTNFPPSYTQRNIRDLLQDI-NVVALSI-RLPSLRFNTSRRFAYIDVTS 168
Query: 79 PQDAANAKEALNFMPINGKPIRIMYSHRDPSIRKSGYGN-----VFIKNLDTS-IDNKAL 132
+DA E LN + I G + S+ +++ + I+NL T +D L
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIXIRNLSTELLDENLL 228
Query: 133 CDTFAAFGTVLSCKVAIDSNGQSKGY----GFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
++F FG++ K+ I + + + F FEN+++A+ A++ N L+ ++++ V
Sbjct: 229 RESFEGFGSIE--KINIPAGQKEHSFNNCCAFXVFENKDSAERALQX-NRSLLGNREISV 285
Query: 189 GL 190
L
Sbjct: 286 SL 287
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 47/75 (62%), Gaps = 5/75 (6%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALN 368
ANLY+ L +++ +++++LFS++G I + ++++DQ G S+G GF F EA A+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 369 EMNGKMIGRKPLYVA 383
+NG+ KPL A
Sbjct: 62 GLNGQ----KPLGAA 72
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFG-TITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
N+YV+ L +T++ ++++++F +G ITS I++ + G SR GF+ F A A++
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 267 LNG 269
LNG
Sbjct: 63 LNG 65
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKM 175
N+++ L ++ K + F+ +G +++ ++ +D + G S+G GF++F+ A+ AIK
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 176 LNG 178
LNG
Sbjct: 63 LNG 65
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
+ +LYV L + +++ ++ LFSQ ++++ R+ DQ+ S G ++ + +A A
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 87 EALNFM-PIN-GKPIRIMYSHRDPS 109
+ LN P+ +PI + +++ +PS
Sbjct: 61 KGLNGQKPLGAAEPITVKFAN-NPS 84
>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 = 46/182 (25%), Positives = 81/182 (44%), Gaps = 28/182 (15%)
Query: 209 VYVNNLAETVTDEDLKKIFG---HFGTITSAI---VMKDSDGKSRCFGFVNFQSPDAAAA 262
+YV N+ +T+E + F G +T A V+ + + F F+ F+S D
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 263 AVEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGAN-LYLKNLDDSI 321
A+ D + + G++ K R Y+ L GA+ L++ L + +
Sbjct: 69 AMAF-------DGIIFQGQSLKI-------------RRPHDYQPLPGAHKLFIGGLPNYL 108
Query: 322 NDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPL 380
ND+++KEL + FG + + ++ D G SKG F + +A+ +NG +G K L
Sbjct: 109 NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 168
Query: 381 YV 382
V
Sbjct: 169 LV 170
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 39/171 (22%), Positives = 80/171 (46%), Gaps = 21/171 (12%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQ-----------VVSVRVCRDQSKRSSLGYAYVNYSN 78
LYVG++ + E + D F+ + V++V++ +D++ +A++ + +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 62
Query: 79 PQDAANAKEALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAA 138
+ A A + + G+ ++I H + G +FI L +++ + + +
Sbjct: 63 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTS 119
Query: 139 FGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
FG + + + DS G SKGY F ++ + AI LNGM + DK++ V
Sbjct: 120 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 77/173 (44%), Gaps = 16/173 (9%)
Query: 118 VFIKNLDTSIDNKALCDTFAA---FGTVLSCK----VAIDSNGQSKGYGFVQFENEEAAQ 170
+++ N+ I +A+ D F A G + +A+ N Q K + F++F + +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETT 67
Query: 171 NAIKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHF 230
A+ +G++ + L +RR Q P +++ L + D+ +K++ F
Sbjct: 68 QAMA-FDGIIFQGQS----LKIRRPHDYQP--LPGAHKLFIGGLPNYLNDDQVKELLTSF 120
Query: 231 GTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKLNGTTNNDKVWYVGRA 282
G + + ++KDS G S+ + F + + A+ LNG DK V RA
Sbjct: 121 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 173
Score = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 35/76 (46%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G L++G L +N+ Q+ +L + + + + +D + S GYA+ Y + A
Sbjct: 95 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 154
Query: 86 KEALNFMPINGKPIRI 101
LN M + K + +
Sbjct: 155 IAGLNGMQLGDKKLLV 170
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 33/95 (34%), Positives = 49/95 (51%), Gaps = 8/95 (8%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ----SKGYGFVQFENEEA 168
SG +FIKNL+ S + L F+ G + SC ++ N S G+GFV+++ E
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 169 AQNAIKMLNGMLINDKQVYVGLFVRRQERAQQNVS 203
AQ A+K L G ++ + L VR ERA + S
Sbjct: 63 AQKALKQLQGHTVDGHK----LEVRISERATKPAS 93
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 4/82 (4%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG----FSKGSGFAAFSMPEEATR 365
+ L++KNL+ S +E LK +FS+ G I SC + ++ S G GF + PE+A +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 366 ALNEMNGKMIGRKPLYVAVAQR 387
AL ++ G + L V +++R
Sbjct: 66 ALKQLQGHTVDGHKLEVRISER 87
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRS---SLGYAYVNYSNPQDA 82
G+ L++ +L + E L +FS+V + S + + ++K S+G+ +V Y P+ A
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 83 ANAKEALNFMPINGKPIRIMYSHR 106
A + L ++G + + S R
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISER 87
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 39/75 (52%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N L V L E L ++FS+ + V + DQ R S G+A+V + N DA AK
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 87 EALNFMPINGKPIRI 101
E N M ++G+ IR+
Sbjct: 75 ERANGMELDGRRIRV 89
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 211 VNNLAETVTDEDLKKIFGHFGTITS-AIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
V L+ T+ DL+++F +G I +IV +SR F FV F++ D A A E+ NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Score = 35.4 bits (80), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 130 KALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
+ L + F+ +G + + D + S+G+ FV FEN + A+ A + NGM ++ +++ V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG-FSKGSGFAAFSMPEEATRAL 367
G +LY D L+E+FS++G I ++ DQ S+G F F ++A A
Sbjct: 22 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 368 NEMNG-KMIGRK 378
NG ++ GR+
Sbjct: 75 ERANGMELDGRR 86
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 46/182 (25%), Positives = 81/182 (44%), Gaps = 28/182 (15%)
Query: 209 VYVNNLAETVTDEDLKKIFG---HFGTITSAI---VMKDSDGKSRCFGFVNFQSPDAAAA 262
+YV N+ +T+E + F G +T A V+ + + F F+ F+S D
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 263 AVEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGAN-LYLKNLDDSI 321
A+ D + + G++ K R Y+ L GA+ L++ L + +
Sbjct: 67 AMAF-------DGIIFQGQSLKI-------------RRPHDYQPLPGAHKLFIGGLPNYL 106
Query: 322 NDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPL 380
ND+++KEL + FG + + ++ D G SKG F + +A+ +NG +G K L
Sbjct: 107 NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 166
Query: 381 YV 382
V
Sbjct: 167 LV 168
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 39/171 (22%), Positives = 80/171 (46%), Gaps = 21/171 (12%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQ-----------VVSVRVCRDQSKRSSLGYAYVNYSN 78
LYVG++ + E + D F+ + V++V++ +D++ +A++ + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 60
Query: 79 PQDAANAKEALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAA 138
+ A A + + G+ ++I H + G +FI L +++ + + +
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTS 117
Query: 139 FGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
FG + + + DS G SKGY F ++ + AI LNGM + DK++ V
Sbjct: 118 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 77/173 (44%), Gaps = 16/173 (9%)
Query: 118 VFIKNLDTSIDNKALCDTFAA---FGTVLSCK----VAIDSNGQSKGYGFVQFENEEAAQ 170
+++ N+ I +A+ D F A G + +A+ N Q K + F++F + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETT 65
Query: 171 NAIKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHF 230
A+ +G++ + L +RR Q P +++ L + D+ +K++ F
Sbjct: 66 QAMA-FDGIIFQGQS----LKIRRPHDYQP--LPGAHKLFIGGLPNYLNDDQVKELLTSF 118
Query: 231 GTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKLNGTTNNDKVWYVGRA 282
G + + ++KDS G S+ + F + + A+ LNG DK V RA
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 35/76 (46%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G L++G L +N+ Q+ +L + + + + +D + S GYA+ Y + A
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 86 KEALNFMPINGKPIRI 101
LN M + K + +
Sbjct: 153 IAGLNGMQLGDKKLLV 168
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQN 171
S + +VF+ +L I + + FA FG + +V D + G+SKGYGFV F N+ A+N
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 172 AIKMLNGMLINDKQVYVGLFVRR 194
AI + G + +Q+ R+
Sbjct: 73 AIVHMGGQWLGGRQIRTNWATRK 95
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 7/85 (8%)
Query: 198 AQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQS 256
Q+ + +V+V +L+ +T ED+K F FG I+ A V+KD + GKS+ +GFV+F +
Sbjct: 7 GQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 257 PDAAAAAVEKLNGTTNNDKVWYVGR 281
A A+ + G W GR
Sbjct: 67 KLDAENAIVHMGGQ------WLGGR 85
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 39/79 (49%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
++VGDL + + F+ ++ RV +D + S GY +V++ N DA NA +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 90 NFMPINGKPIRIMYSHRDP 108
+ G+ IR ++ R P
Sbjct: 78 GGQWLGGRQIRTNWATRKP 96
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNE 369
++++ +L I E +K F+ FG I+ +V+ D G SKG GF +F +A A+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 370 MNGKMIGRKPLYVAVAQRK 388
M G+ +G + + A RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
>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 = 24/61 (39%), Positives = 37/61 (60%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
V+V NL V +E L ++F G +T + KD +GK + FGFV F+ P++ + A+ LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 269 G 269
G
Sbjct: 79 G 79
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+++VG+LE V E LY+LF Q + V +C+D+ + + +V + +P+ + A
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK-SFGFVCFKHPESVSYAIAL 76
Query: 89 LNFMPINGKPIRI 101
LN + + G+PI +
Sbjct: 77 LNGIRLYGRPINV 89
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 39/72 (54%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
+++ NL+ + +E L ELF + G +T + D+ G K GF F PE + A+ +N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 372 GKMIGRKPLYVA 383
G + +P+ V+
Sbjct: 79 GIRLYGRPINVS 90
Score = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 38/71 (53%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
VF+ NL+ + + L + F G + + D G+ K +GFV F++ E+ AI +LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 178 GMLINDKQVYV 188
G+ + + + V
Sbjct: 79 GIRLYGRPINV 89
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L Y +FSQ Q++ + V R R G A+V +
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIF 58
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 6/95 (6%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS+FG I ++V + +G F F AT A
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARLQAQFAQ 401
L M G KP+ + A+ + A+++ F +
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVE 102
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 50/105 (47%), Gaps = 7/105 (6%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 67
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLK 308
+ + G DK + A+ ++ A ++ F ER + EK K
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF-VERDRKREKRK 111
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 45/79 (56%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N +L V L Q++ + +LY LF + + + R+ RD S GYA+V++++ D+ A
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 87 EALNFMPINGKPIRIMYSH 105
+ LN + + K +++ Y+
Sbjct: 63 KVLNGITVRNKRLKVSYAR 81
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKM 175
N+ + L + ++ L F A G + +C++ D G S GY FV F +E +Q AIK+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 176 LNGMLINDKQVYV 188
LNG+ + +K++ V
Sbjct: 65 LNGITVRNKRLKV 77
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALN 368
NL + L + D +L LF G I +C++M D + G+S G F F+ ++ RA+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 369 EMNGKMIGRKPLYVAVAQ 386
+NG + K L V+ A+
Sbjct: 64 VLNGITVRNKRLKVSYAR 81
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVE 265
TN+ VN L + +TD +L +F G I + +M+D G S + FV+F S + A++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 266 KLNGTTNNDKVWYVGRAQKRAE 287
LNG T +K V A+ E
Sbjct: 64 VLNGITVRNKRLKVSYARPGGE 85
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 11/90 (12%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
++V NLA TVT+E L+K F FG + +KD + F++F D A A+E++N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 269 GT----TNNDKVWYVGRAQKRAEREADLRA 294
G N + V+ QKR ER+A +A
Sbjct: 67 GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 51/90 (56%), Gaps = 11/90 (12%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L+++NL +++ +E L++ FS+FG + K + D F F + A +A+ EMN
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY-------AFIHFDERDGAVKAMEEMN 66
Query: 372 GKMIGRKPLYVAVA----QRKEERKARLQA 397
GK + + + + A Q+++ERKA+ QA
Sbjct: 67 GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 23 SGYGNVS-LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQD 81
SG V L+V +L V E L FSQ ++ V+ +D YA++++
Sbjct: 6 SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDG 57
Query: 82 AANAKEALNFMPINGKPIRIMYS 104
A A E +N + G+ I I+++
Sbjct: 58 AVKAMEEMNGKDLEGENIEIVFA 80
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 13/88 (14%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+F++NL ++ + L F+ FG + K + K Y F+ F+ + A A++ +N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMN 66
Query: 178 GMLINDKQVYVGLFV-----RRQERAQQ 200
G + + + + +F +R+ER Q
Sbjct: 67 GKDLEGENIEI-VFAKPPDQKRKERKAQ 93
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L Y +FSQ Q++ + V R R G A+V +
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIF 59
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 60 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 52/210 (24%), Positives = 84/210 (40%), Gaps = 64/210 (30%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS+FG I ++V + +G F F AT A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 367 LNEMNGKMIGRKPLYVAVAQ------------------RKEERKARLQAQFAQIRAP--G 406
L M G KP+ + A+ ++E+RK + Q A +A G
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128
Query: 407 GMSPLASGIPGYHHGAPRL--GPQQLYY---------------------GQGTPGLMPPQ 443
G +P+ + G G P + P+ +++ GQ PG MPP
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPP- 187
Query: 444 AAGYGFQQQVFPGLRPGG-------PNYIM 466
QQ+ PG P PN+I+
Sbjct: 188 -------QQLMPGQMPPAQPLSENPPNHIL 210
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 50/105 (47%), Gaps = 7/105 (6%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 68
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLK 308
+ + G DK + A+ ++ A ++ F ER + EK K
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV-ERDRKREKRK 112
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 62/294 (21%), Positives = 111/294 (37%), Gaps = 37/294 (12%)
Query: 94 INGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNG 153
++ + IR H + R + I+ L + N+ + D + + + C V
Sbjct: 3 LDPEEIRKRLEHTERQFRNRR--KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----D 54
Query: 154 QSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNN 213
+ KG FV N E A+ AI + + ++++ V L P + V N
Sbjct: 55 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL------------QPTDALLCVAN 102
Query: 214 LAETVTDEDLKKIFGHFGTITSA-IVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
L ++T + +++ FG++ +V + G+S+ +GF + D+AA A L G
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 162
Query: 273 NDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSIND-EKLKELFS 331
+ YV A L ++ L + L ND + L S
Sbjct: 163 GPRTLYVHWTDAGQLTPALLHSR---------------CLCVDRLPPGFNDVDALCRALS 207
Query: 332 EFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVA 385
+ T C++ Q G KG + E A A + +G +G L V+
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 35/163 (21%), Positives = 69/163 (42%), Gaps = 6/163 (3%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L V +L ++ + Q +L + + + S GY + Y AA AK L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 90 NFMPINGKPIRIMYS---HRDPSIRKSGYGNVFIKNLDTSI-DNKALCDTFAAFGTVLSC 145
P+ + + + ++ P++ S + + L D ALC +A + C
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSR--CLCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 146 KVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
++A +GQ KG+ +++E E A+ A + +G+ + + V
Sbjct: 216 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 62/294 (21%), Positives = 111/294 (37%), Gaps = 37/294 (12%)
Query: 94 INGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNG 153
++ + IR H + R + I+ L + N+ + D + + + C V
Sbjct: 1 LDPEEIRKRLEHTERQFRNRR--KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----D 52
Query: 154 QSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNN 213
+ KG FV N E A+ AI + + ++++ V L P + V N
Sbjct: 53 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL------------QPTDALLCVAN 100
Query: 214 LAETVTDEDLKKIFGHFGTITSA-IVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
L ++T + +++ FG++ +V + G+S+ +GF + D+AA A L G
Sbjct: 101 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 160
Query: 273 NDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSIND-EKLKELFS 331
+ YV A L ++ L + L ND + L S
Sbjct: 161 GPRTLYVHWTDAGQLTPALLHSR---------------CLCVDRLPPGFNDVDALCRALS 205
Query: 332 EFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVA 385
+ T C++ Q G KG + E A A + +G +G L V+
Sbjct: 206 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 259
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 35/165 (21%), Positives = 69/165 (41%), Gaps = 6/165 (3%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L V +L ++ + Q +L + + + S GY + Y AA AK L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 90 NFMPINGKPIRIMYS---HRDPSIRKSGYGNVFIKNLDTSI-DNKALCDTFAAFGTVLSC 145
P+ + + + ++ P++ S + + L D ALC +A + C
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPALLHSR--CLCVDRLPPGFNDVDALCRALSAVHSPTFC 213
Query: 146 KVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGL 190
++A +GQ KG+ +++E E A+ A + +G+ + + V
Sbjct: 214 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 258
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 40/73 (54%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
S++VG++ E QL D+FS+V VVS R+ D+ GY + Y + + A +A
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 89 LNFMPINGKPIRI 101
LN +G+ +R+
Sbjct: 70 LNGREFSGRALRV 82
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 108 PSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENE 166
P++ +S +VF+ N+ + L D F+ G V+S ++ D G+ KGYGF +++++
Sbjct: 2 PAVDRS-LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60
Query: 167 EAAQNAIKMLNG 178
E A +A++ LNG
Sbjct: 61 ETALSAMRNLNG 72
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 1/89 (1%)
Query: 202 VSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSD-GKSRCFGFVNFQSPDAA 260
V +V+V N+ T+E LK IF G + S ++ D + GK + +GF +Q + A
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 261 AAAVEKLNGTTNNDKVWYVGRAQKRAERE 289
+A+ LNG + + V A +E
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASEKNKE 92
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 48/87 (55%), Gaps = 4/87 (4%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNE 369
++++ N+ +E+LK++FSE G + S +++ D+ G KG GF + E A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 370 MNGKMIGRKPLYV---AVAQRKEERKA 393
+NG+ + L V A + KEE K+
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEELKS 96
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 62/294 (21%), Positives = 111/294 (37%), Gaps = 37/294 (12%)
Query: 94 INGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNG 153
++ + IR H + R + I+ L + N+ + D + + + C V
Sbjct: 3 LDPEEIRKRLEHTERQFRNRR--KILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----D 54
Query: 154 QSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNN 213
+ KG FV N E A+ AI + + ++++ V L P + V N
Sbjct: 55 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL------------QPTDALLCVAN 102
Query: 214 LAETVTDEDLKKIFGHFGTITSA-IVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNGTTN 272
L ++T + +++ FG++ +V + G+S+ +GF + D+AA A L G
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 162
Query: 273 NDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSIND-EKLKELFS 331
+ YV A L ++ L + L ND + L S
Sbjct: 163 GPRTLYVHWTDAGQLTPALLHSR---------------CLCVDRLPPGFNDVDALCRALS 207
Query: 332 EFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVA 385
+ T C++ Q G KG + E A A + +G +G L V+
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 40/170 (23%), Positives = 70/170 (41%), Gaps = 16/170 (9%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L V +L ++ + Q +L + + + S GY + Y AA AK L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 90 NFMPINGKPI--RIMYSHRD------PSIRKSGYGNVFIKNLDTSI-DNKALCDTFAAFG 140
GKP+ R +Y H P++ S + + L D ALC +A
Sbjct: 158 L-----GKPLGPRTLYVHWTDAGQLTPALLHSR--CLCVDRLPPGFNDVDALCRALSAVH 210
Query: 141 TVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGL 190
+ C++A +GQ KG+ +++E E A+ A + +G+ + + V
Sbjct: 211 SPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L Y +FSQ Q++ + V R R G A+V +
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIF 59
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 60 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS+FG I ++V + +G F F AT A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 367 LNEMNGKMIGRKPLYVAVAQ 386
L M G KP+ + A+
Sbjct: 69 LRSMQGFPFYDKPMRIQYAK 88
Score = 37.0 bits (84), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 68
Query: 264 VEKLNGTTNNDK 275
+ + G DK
Sbjct: 69 LRSMQGFPFYDK 80
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 42/76 (55%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALN 368
GA L + NLD ++D ++ELF+EFGT+ V D+ G S G+ F +A +A+
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
Query: 369 EMNGKMIGRKPLYVAV 384
+ G + +P+ + +
Sbjct: 148 QYKGVPLDGRPMDIQL 163
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+ + NLD + + + + FA FGT+ V D +G+S G V FE A A+K
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 178 GMLINDKQVYVGLFV 192
G+ ++ + + + L
Sbjct: 151 GVPLDGRPMDIQLVA 165
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKE 87
L V +L+ V+++ + +LF++ + V D+S RS LG A V++ DA A +
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRADALKAMK 147
Query: 88 ALNFMPINGKPIRI 101
+P++G+P+ I
Sbjct: 148 QYKGVPLDGRPMDI 161
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
+ V+NL V+D D++++F FGT+ A V D G+S V+F+ A A+++
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148
Query: 267 LNGT 270
G
Sbjct: 149 YKGV 152
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
++V L + TDED++K+F FGTI V++ DG S+ FV FQ+ A AA+ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 269 GT 270
+
Sbjct: 75 SS 76
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L++ L DE ++++F FGTI C V+ G SKG F F EA A+N ++
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Score = 36.2 bits (82), Expect = 0.057, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 23/42 (54%)
Query: 136 FAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
F FGT+ C V +G SKG FV+F+ AQ AI L+
Sbjct: 33 FEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 41/73 (56%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L + NLD ++D ++ELF+EFGT+ V D+ G S G+ F +A +A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 372 GKMIGRKPLYVAV 384
G + +P+ + +
Sbjct: 91 GVPLDGRPMNIQL 103
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+ + NLD + + + + FA FGT+ V D +G+S G V FE + A A+K N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 178 GMLINDKQVYVGL 190
G+ ++ + + + L
Sbjct: 91 GVPLDGRPMNIQL 103
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L V +L+ V+++ + +LF++ + V D+S RS LG A V++ DA A +
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS-LGTADVHFERKADALKAMKQY 89
Query: 90 NFMPINGKPIRI 101
N +P++G+P+ I
Sbjct: 90 NGVPLDGRPMNI 101
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 35/62 (56%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
+ V+NL V+D D++++F FGT+ A V D G+S V+F+ A A+++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 269 GT 270
G
Sbjct: 91 GV 92
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALN 368
GA L + NLD ++D ++ELF+EFGT+ V D+ G S G+ F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 369 EMNGKMIGRKPL 380
+ G + +P+
Sbjct: 95 QYKGVPLDGRPM 106
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+ + NLD + + + + FA FGT+ V D +G+S G V FE A A+K
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 178 GMLINDKQVYVGL 190
G+ ++ + + + L
Sbjct: 98 GVPLDGRPMDIQL 110
Score = 36.6 bits (83), Expect = 0.039, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L V +L+ V+++ + +LF++ + V D+S RS LG A V++ DA A +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRADALKAMKQY 96
Query: 90 NFMPINGKPIRI 101
+P++G+P+ I
Sbjct: 97 KGVPLDGRPMDI 108
Score = 35.8 bits (81), Expect = 0.072, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 33/59 (55%)
Query: 211 VNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
V+NL V+D D++++F FGT+ A V D G+S V+F+ A A+++ G
Sbjct: 40 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKG 98
>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 = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
VF+ +D +D + FA +G+V K+ D G SKGYGFV F N+ Q ++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-- 68
Query: 177 NGMLINDKQVYVGLFVRRQ 195
+ + + K++ +G +R+Q
Sbjct: 69 SQINFHGKKLKLGPAIRKQ 87
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 30/47 (63%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAF 357
+++ +D +++ +++ F+ +G++ K++ D+ G SKG GF +F
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 29/58 (50%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVE 265
V+V + + + +++ F +G++ ++ D G S+ +GFV+F + VE
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALN 368
GA L + NLD ++D ++ELF+EFGT+ V D+ G S G+ F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 369 EMNGKMIGRKPL 380
+ G + +P+
Sbjct: 95 QYKGVPLDGRPM 106
Score = 38.1 bits (87), Expect = 0.016, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+ + NLD + + + + FA FGT+ V D +G+S G V FE A A+K
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 178 GMLINDKQVYVGL 190
G+ ++ + + + L
Sbjct: 98 GVPLDGRPMDIQL 110
Score = 36.6 bits (83), Expect = 0.040, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L V +L+ V+++ + +LF++ + V D+S RS LG A V++ DA A +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRADALKAMKQY 96
Query: 90 NFMPINGKPIRI 101
+P++G+P+ I
Sbjct: 97 KGVPLDGRPMDI 108
Score = 35.8 bits (81), Expect = 0.074, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 33/59 (55%)
Query: 211 VNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
V+NL V+D D++++F FGT+ A V D G+S V+F+ A A+++ G
Sbjct: 40 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKG 98
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 202 VSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG-KSRCFGFVNFQSPDAA 260
++P + VYV+NL ++T+ DL +IF +G + +MKD D KS+ F+ F D+A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 261 AAAVEKLN 268
+N
Sbjct: 72 QNCTRAIN 79
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 41/72 (56%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
++YV +L ++ + LY +FS+ +VV V + +D+ R S G A++ + + A N A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 89 LNFMPINGKPIR 100
+N + G+ I+
Sbjct: 78 INNKQLFGRVIK 89
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNG-QSKGYGFVQFENEEAAQNAIKML 176
V++ NL S+ N L F+ +G V+ + D + +SKG F+ F ++++AQN +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA- 77
Query: 177 NGMLINDKQVY 187
IN+KQ++
Sbjct: 78 ----INNKQLF 84
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
VF+ +D +D + FA +G+V K+ D G SKGYGFV F N+ Q ++
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-- 69
Query: 177 NGMLINDKQVYVGLFVRRQ 195
+ + + K++ +G +R+Q
Sbjct: 70 SQINFHGKKLKLGPAIRKQ 88
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 30/47 (63%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAF 357
+++ +D +++ +++ F+ +G++ K++ D+ G SKG GF +F
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 29/58 (50%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVE 265
V+V + + + +++ F +G++ ++ D G S+ +GFV+F + VE
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 69
>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 = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 47/88 (53%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+LYVG+L E Q+Y+LFS+ + + + D+ K+++ G+ +V Y + DA NA
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 89 LNFMPINGKPIRIMYSHRDPSIRKSGYG 116
+N ++ + IR + R+ G G
Sbjct: 101 INGTRLDDRIIRTDWDAGFKEGRQYGRG 128
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 31/116 (26%), Positives = 52/116 (44%), Gaps = 9/116 (7%)
Query: 193 RRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRC-FGF 251
R Q+ + K +YV NL+ T+E + ++F G I I+ D K+ C F F
Sbjct: 26 RGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCF 85
Query: 252 VNFQSPDAAAAAVEKLNGTTNNDKV--------WYVGRAQKRAEREADLRAKFEQE 299
V + S A A+ +NGT +D++ + GR R +R ++ Q+
Sbjct: 86 VEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQD 141
Score = 28.9 bits (63), Expect = 8.6, Method: Composition-based stats.
Identities = 14/68 (20%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSK-GYGFVQFENEEAAQNAIKML 176
+++ NL + + + F+ G + + +D ++ G+ FV++ + A+NA++ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 177 NGMLINDK 184
NG ++D+
Sbjct: 102 NGTRLDDR 109
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 30/83 (36%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 311 NLYLKNLDDSINDEKLKELFSE-FGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNE 369
+L++ +L ++D L E F + + + KV++DQ G SKG GF F+ E RAL E
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 370 MNGKM-IGRKPLYVAVAQRKEER 391
G + +G KP+ ++VA K R
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93
Score = 37.4 bits (85), Expect = 0.023, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 117 NVFIKNLDTSIDNKALCDTFA-AFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKM 175
++F+ +L +D+ L + F + + KV +D G SKGYGFV+F +E + A+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 176 LNGML-INDKQVYVGLFVRRQERAQ 199
G + + K V + + + + R +
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVK 95
Score = 34.3 bits (77), Expect = 0.23, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQV-AQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA-K 86
SL+VGDL +V++ LY+ F +V +V DQ+ S GY +V +++ + A
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSK-GYGFVKFTDELEQKRALT 69
Query: 87 EALNFMPINGKPIRI 101
E + + KP+R+
Sbjct: 70 ECQGAVGLGSKPVRL 84
>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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIF 59
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 60 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARLQ 396
L M G KP+ + A+ + A+++
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 37.7 bits (86), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 68
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFE 297
+ + G DK + + A+ ++D+ AK +
Sbjct: 69 LRSMQGFPFYDKPMRI----QYAKTDSDIIAKMK 98
>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 = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIF 58
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 6/94 (6%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARLQAQFA 400
L M G KP+ + A+ + A+++ F
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 101
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 6/93 (6%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 67
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKF 296
+ + G DK + A+ ++ A ++ F
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKM 175
+VF+ +L I A+ FA FG + +V D + G+SKGYGFV F N+ A+NAI+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 176 LNGMLINDKQVYVGLFVRR 194
+ G + +Q+ R+
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 41/79 (51%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
++VGDL + + + F+ ++ RV +D + S GY +V++ N DA NA + +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 90 NFMPINGKPIRIMYSHRDP 108
+ G+ IR ++ R P
Sbjct: 69 GGQWLGGRQIRTNWATRKP 87
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 333 FGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYVAVAQRK 388
FG I+ +V+ D G SKG GF +F +A A+ +M G+ +G + + A RK
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEK 266
+V+V +L+ +T + F FG I+ A V+KD + GKS+ +GFV+F + A A+++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 267 LNG 269
+ G
Sbjct: 68 MGG 70
>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 = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIF 59
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 60 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 93
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARLQ 396
L M G KP+ + A+ + A+++
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 37.7 bits (86), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 68
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFE 297
+ + G DK + + A+ ++D+ AK +
Sbjct: 69 LRSMQGFPFYDKPMRI----QYAKTDSDIIAKMK 98
>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 = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIF 58
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARLQ 396
L M G KP+ + A+ + A+++
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 67
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFE 297
+ + G DK + + A+ ++D+ AK +
Sbjct: 68 LRSMQGFPFYDKPMRI----QYAKTDSDIIAKMK 97
>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 = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIF 58
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 92
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARL 395
L M G KP+ + A+ + A++
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96
Score = 37.4 bits (85), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 10/92 (10%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 67
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAK 295
+ + G DK + + A+ ++D+ AK
Sbjct: 68 LRSMQGFPFYDKPMRI----QYAKTDSDIIAK 95
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
++V+N+ D DL+++FG FG I ++ + G S+ FGFV F++ A A EKL+
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 90
Query: 269 GTTNNDKVWYVGRAQKRA 286
GT + V A R
Sbjct: 91 GTVVEGRKIEVNNATARV 108
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 40/68 (58%), Gaps = 2/68 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L++ N+ D L+++F +FG I +++ ++ G SKG GF F +A RA +++
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 90
Query: 372 GKMI-GRK 378
G ++ GRK
Sbjct: 91 GTVVEGRK 98
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 120 IKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGM 179
+ N+ + L F FG +L ++ + G SKG+GFV FEN A A + L+G
Sbjct: 34 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 92
Query: 180 LINDKQVYV 188
++ +++ V
Sbjct: 93 VVEGRKIEV 101
>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 = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 37/68 (54%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L + NLD ++D ++ELF+EFGT+ V D+ G S G+ F +A +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 372 GKMIGRKP 379
G + +P
Sbjct: 92 GVPLDGRP 99
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L V +L+ V+++ + +LF++ + V D+S RS LG A V++ DA A +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS-LGTADVHFERKADALKAXKQY 90
Query: 90 NFMPINGKPIRI 101
N +P++G+P I
Sbjct: 91 NGVPLDGRPXNI 102
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 35/67 (52%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+ + NLD + + + + FA FGT+ V D +G+S G V FE + A A K N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 178 GMLINDK 184
G+ ++ +
Sbjct: 92 GVPLDGR 98
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 211 VNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLNG 269
V+NL V+D D++++F FGT+ A V D G+S V+F+ A A ++ NG
Sbjct: 34 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNG 92
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
++V+N+ D DL+++FG FG I ++ + G S+ FGFV F++ A A EKL+
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 269 GTTNNDKVWYVGRAQKRA 286
GT + V A R
Sbjct: 77 GTVVEGRKIEVNNATARV 94
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 40/68 (58%), Gaps = 2/68 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L++ N+ D L+++F +FG I +++ ++ G SKG GF F +A RA +++
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 372 GKMI-GRK 378
G ++ GRK
Sbjct: 77 GTVVEGRK 84
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 120 IKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGM 179
+ N+ + L F FG +L ++ + G SKG+GFV FEN A A + L+G
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 180 LINDKQVYV 188
++ +++ V
Sbjct: 79 VVEGRKIEV 87
>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 = 25/68 (36%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 204 PKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
P VYV NL +L++ FG++G + S V ++ G F FV F+ P AA A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADA 126
Query: 264 VEKLNGTT 271
V +L+G T
Sbjct: 127 VRELDGRT 134
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
+ +YVG+L N N+++L F + SV V R+ G+A+V + +P+DAA+A
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAV 127
Query: 87 EALNFMPINGKPIRIMYSH 105
L+ + G +R+ S+
Sbjct: 128 RELDGRTLCGCRVRVELSN 146
Score = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
V++ NL + + L F +G + S VA + G+ FV+FE+ A +A++ L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP----PGFAFVEFEDPRDAADAVRELD 131
Query: 178 GMLINDKQVYVGL 190
G + +V V L
Sbjct: 132 GRTLCGCRVRVEL 144
>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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 44/80 (55%)
Query: 22 PSGYGNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQD 81
P G SL V +L + L +F + +V V + RD+ + S G+A+V + + +D
Sbjct: 42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 82 AANAKEALNFMPINGKPIRI 101
A +A +A++ ++G+ +R+
Sbjct: 102 AEDAMDAMDGAVLDGRELRV 121
Score = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 206 FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSPDAAAAAV 264
T++ V+NL + + L+++F +G + + +D K SR F FV F A A+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 265 EKLNG 269
+ ++G
Sbjct: 107 DAMDG 111
Score = 36.2 bits (82), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 114 GYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNA 172
G ++ + NL L F +G V + D +S+G+ FV+F ++ A++A
Sbjct: 46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105
Query: 173 IKMLNGMLINDKQVYV 188
+ ++G +++ +++ V
Sbjct: 106 MDAMDGAVLDGRELRV 121
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGF-SKGSGFAAFSMPEEATRALN 368
+L + NL + + L+ +F ++G + + D++ S+G F F +A A++
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 369 EMNGKMIGRKPLYVAVAQ 386
M+G ++ + L V +A+
Sbjct: 108 AMDGAVLDGRELRVQMAR 125
>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 = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKM- 175
+FI L K L D F+ FG V+ C + +D G+S+G+GFV F+ E+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 176 ---LNGMLINDKQ 185
LNG +I+ K+
Sbjct: 62 EHKLNGKVIDPKR 74
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNE- 369
+++ L + LK+ FS+FG + C + +D G S+G GF F E + +++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 370 ---MNGKMIGRK 378
+NGK+I K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 36.6 bits (83), Expect = 0.038, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVE-- 265
+++ L+ T +DLK F FG + + D G+SR FGFV F+ ++ ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 266 --KLNGTTNNDK 275
KLNG + K
Sbjct: 62 EHKLNGKVIDPK 73
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 7/93 (7%)
Query: 22 PSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYS 77
P N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFK 57
Query: 78 NPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA ++ P KP+RI Y+ D I
Sbjct: 58 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDI 90
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT A
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 65
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARLQ 396
L M G KP+ + A+ + A+++
Sbjct: 66 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 95
Score = 37.7 bits (86), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 8 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 65
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFE 297
+ + G DK + + A+ ++D+ AK +
Sbjct: 66 LRSMQGFPFYDKPMRI----QYAKTDSDIIAKMK 95
>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 = 25/68 (36%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 204 PKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
P VYV NL +L++ FG++G + S V ++ G F FV F+ P AA A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADA 126
Query: 264 VEKLNGTT 271
V L+G T
Sbjct: 127 VRDLDGRT 134
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
+ +YVG+L N N+++L F + SV V R+ G+A+V + +P+DAA+A
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAV 127
Query: 87 EALNFMPINGKPIRIMYSH 105
L+ + G +R+ S+
Sbjct: 128 RDLDGRTLCGCRVRVELSN 146
Score = 30.0 bits (66), Expect = 4.0, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
V++ NL + + L F +G + S VA + G+ FV+FE+ A +A++ L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP----PGFAFVEFEDPRDAADAVRDLD 131
Query: 178 GMLINDKQVYVGL 190
G + +V V L
Sbjct: 132 GRTLCGCRVRVEL 144
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/189 (21%), Positives = 84/189 (44%), Gaps = 37/189 (19%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQ-----------VVSVRVCRDQSKRSSLGYAYVNYSN 78
LYVG++ + E + D F+ + V++V++ +D++ +A++ + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 60
Query: 79 PQDAANAKEALNFMPINGKPIRIMYSH---------RDPSIRKSGYGN---------VFI 120
+ A A + + G+ ++I H +PS+ G + +FI
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 121 KNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKMLNGM 179
L +++ + + +FG + + + DS G SKGY F ++ + AI LNGM
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Query: 180 LINDKQVYV 188
+ DK++ V
Sbjct: 180 QLGDKKLLV 188
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 45/189 (23%), Positives = 79/189 (41%), Gaps = 22/189 (11%)
Query: 209 VYVNNLAETVTDEDLKKIFG---HFGTITSAI---VMKDSDGKSRCFGFVNFQSPDAAAA 262
+YV N+ +T+E + F G +T A V+ + + F F+ F+S D
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 263 AVEKLNGTTNNDKVWYVGRAQK--RAEREADLRAKFEQERI------SRYEKLKGANLYL 314
A+ D + + G++ K R L E + S L++
Sbjct: 67 AMAF-------DGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 315 KNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEMNGK 373
L + +ND+++KEL + FG + + ++ D G SKG F + +A+ +NG
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Query: 374 MIGRKPLYV 382
+G K L V
Sbjct: 180 QLGDKKLLV 188
Score = 35.4 bits (80), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKL 267
+++ L + D+ +K++ FG + + ++KDS G S+ + F + + A+ L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 268 NGTTNNDKVWYVGRAQKRAE 287
NG DK V RA A+
Sbjct: 177 NGMQLGDKKLLVQRASVGAK 196
>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: Composition-based stats.
Identities = 30/80 (37%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 206 FTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSD-GKSRCFGFVNFQSPDAAAAAV 264
FT ++V L TD L+K F FG I A+V+ D GKSR +GFV AA A
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Query: 265 EKLN----GTTNNDKVWYVG 280
+ N G N + Y+G
Sbjct: 77 KDPNPIIDGRKANVNLAYLG 96
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 111 RKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAA 169
+ + + +F+ L + +L F FG + V D G+S+GYGFV + AA
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 170 QNAIK----MLNGMLINDKQVYVG 189
+ A K +++G N Y+G
Sbjct: 73 ERACKDPNPIIDGRKANVNLAYLG 96
Score = 33.1 bits (74), Expect = 0.45, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
+++ L D L++ F FG I V+ D Q G S+G GF + A RA +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 371 NGKMIGRK 378
N + GRK
Sbjct: 80 NPIIDGRK 87
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 7/88 (7%)
Query: 27 NVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDA 82
N ++Y+ ++ + + +L Y LFSQ VV + + R G A+V + +
Sbjct: 6 NHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMR---GQAFVIFKELGSS 62
Query: 83 ANAKEALNFMPINGKPIRIMYSHRDPSI 110
NA L P GKP+RI Y+ D I
Sbjct: 63 TNALRQLQGFPFYGKPMRIQYAKTDSDI 90
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 201 NVSPKFTNVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQS 256
++ P T +Y+NN+ + + E+LK+ +F FG + + +K K R FV F+
Sbjct: 2 DIRPNHT-IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTM--KMRGQAFVIFKE 58
Query: 257 PDAAAAAVEKLNG 269
++ A+ +L G
Sbjct: 59 LGSSTNALRQLQG 71
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEM 370
L+++NL + ++E L++LFS +G ++ +D KG F F PE A +A E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 371 NGKMIGRKPLYVAVAQRKEE 390
+G++ + L+V + K+E
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKL 267
++V NL+ T ++EDL+K+F +G ++ DS K + F FV F P+ A A ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 268 NGTTNNDKVWYV 279
+G ++ +V
Sbjct: 71 DGQVFQGRMLHV 82
Score = 37.4 bits (85), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F++NL + + L F+A+G + IDS + KG+ FV F E A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 177 NGMLINDKQVYVGLFVRRQERAQQNVS 203
+G + + ++V ++E +Q S
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQSGPS 97
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 36/85 (42%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V +L +E L LFS + + D + G+A+V + P+ A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSG 114
+ G+ + ++ S +SG
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQSG 95
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/91 (20%), Positives = 44/91 (48%), Gaps = 1/91 (1%)
Query: 99 IRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKG 157
+++ H DP+ + + +F+ ++ L F +G + + +G+ +G
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 158 YGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
Y F+++E+E +A K +G I+ ++V V
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/93 (20%), Positives = 45/93 (48%), Gaps = 1/93 (1%)
Query: 99 IRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKG 157
+++ H DP+ + + +F+ ++ L F +G + + +G+ +G
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 158 YGFVQFENEEAAQNAIKMLNGMLINDKQVYVGL 190
Y F+++E+E +A K +G I+ ++V V +
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 178
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 27 NVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDA 82
N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V + A
Sbjct: 5 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSA 61
Query: 83 ANAKEALNFMPINGKPIRIMYSHRDPSI 110
NA ++ P KP+RI Y+ D I
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYAKTDSDI 89
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 311 NLYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRA 366
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT A
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNA 64
Query: 367 LNEMNGKMIGRKPLYVAVAQRKEERKARLQ 396
L M G KP+ + A+ + A+++
Sbjct: 65 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 94
Score = 37.4 bits (85), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 208 NVYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 64
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFE 297
+ + G DK + + A+ ++D+ AK +
Sbjct: 65 LRSMQGFPFYDKPMRI----QYAKTDSDIIAKMK 94
>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 = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+LYVG+L E Q+Y+LFS+ + + + D+ K ++ G+ +V Y + DA NA
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAENAMRY 78
Query: 89 LNFMPINGKPIR 100
+N ++ + IR
Sbjct: 79 INGTRLDDRIIR 90
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 193 RRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRC-FGF 251
R Q+ + K +YV NL+ T+E + ++F G I I+M K+ C F F
Sbjct: 5 RGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKK-IIMGLDKMKTACGFCF 63
Query: 252 VNFQSPDAAAAAVEKLNGTTNNDKV 276
V + S A A+ +NGT +D++
Sbjct: 64 VEYYSRADAENAMRYINGTRLDDRI 88
Score = 34.3 bits (77), Expect = 0.24, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 297 EQERISRYEKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAA 356
EQE++ + K LY+ NL +E++ ELFS+ G I + +D+ + G F
Sbjct: 10 EQEKLLK----KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVE 65
Query: 357 FSMPEEATRALNEMNG 372
+ +A A+ +NG
Sbjct: 66 YYSRADAENAMRYING 81
Score = 33.1 bits (74), Expect = 0.45, Method: Composition-based stats.
Identities = 14/67 (20%), Positives = 36/67 (53%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+++ NL + + + F+ G + + +D + G+ FV++ + A+NA++ +N
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 178 GMLINDK 184
G ++D+
Sbjct: 81 GTRLDDR 87
>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 = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 27 NVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDA 82
N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V + A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSA 59
Query: 83 ANAKEALNFMPINGKPIRIMYSHRDPSI 110
NA ++ P KP+RI Y+ D I
Sbjct: 60 TNALRSMQGFPFYDKPMRIQYAKTDSDI 87
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 312 LYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRAL 367
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT AL
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNAL 63
Query: 368 NEMNGKMIGRKPLYVAVAQ 386
M G KP+ + A+
Sbjct: 64 RSMQGFPFYDKPMRIQYAK 82
Score = 37.4 bits (85), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 10/91 (10%)
Query: 209 VYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAV 264
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A+
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 63
Query: 265 EKLNGTTNNDKVWYVGRAQKRAEREADLRAK 295
+ G DK + + A+ ++D+ AK
Sbjct: 64 RSMQGFPFYDKPMRI----QYAKTDSDIIAK 90
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 37/67 (55%)
Query: 204 PKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
P ++V L + +++D++++F FG I +++ DG S+ FV + S A AA
Sbjct: 13 PSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAA 72
Query: 264 VEKLNGT 270
+ L+G+
Sbjct: 73 INALHGS 79
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L++ L+ +++ ++ LF FG I C ++ G SKG F +S EA A+N ++
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 372 G 372
G
Sbjct: 78 G 78
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 108 PSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEE 167
PS RK +F+ L+ + F AFG + C + +G SKG FV++ +
Sbjct: 13 PSHRK-----LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHA 67
Query: 168 AAQNAIKMLNG 178
AQ AI L+G
Sbjct: 68 EAQAAINALHG 78
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIF 58
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA + P KP RI Y+ D I
Sbjct: 59 KEVSSATNALRSXQGFPFYDKPXRIQYAKTDSDI 92
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 10/91 (10%)
Query: 209 VYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAV 264
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 68
Query: 265 EKLNGTTNNDKVWYVGRAQKRAEREADLRAK 295
G DK + + A+ ++D+ AK
Sbjct: 69 RSXQGFPFYDKPXRI----QYAKTDSDIIAK 95
>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 = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNY 76
VP N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIF 59
Query: 77 SNPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA + P KP RI Y+ D I
Sbjct: 60 KEVSSATNALRSXQGFPFYDKPXRIQYAKTDSDI 93
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 10/91 (10%)
Query: 209 VYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAV 264
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A+
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 69
Query: 265 EKLNGTTNNDKVWYVGRAQKRAEREADLRAK 295
G DK + + A+ ++D+ AK
Sbjct: 70 RSXQGFPFYDKPXRI----QYAKTDSDIIAK 96
>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 = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 116 GNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSN-GQSKGYGFVQFENEEAAQNAIK 174
G F+ L K L D F FG V+ C + D N G+S+G+GF+ F++ + + +
Sbjct: 12 GKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLD 71
Query: 175 M----LNGMLINDKQ 185
L+G +I+ K+
Sbjct: 72 QKEHRLDGRVIDPKK 86
Score = 37.0 bits (84), Expect = 0.032, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 210 YVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSD-GKSRCFGFVNFQSPDAAAAAVEKL 267
+V L+ + +DLK F FG + + D + G+SR FGF+ F+ AA+VEK+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD----AASVEKV 69
Score = 33.1 bits (74), Expect = 0.47, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 313 YLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNEMN 371
++ L + + LK+ F++FG + C + D + G S+G GF F + L++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 372 GKMIGR 377
++ GR
Sbjct: 75 HRLDGR 80
Score = 29.6 bits (65), Expect = 5.9, Method: Composition-based stats.
Identities = 15/60 (25%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 31 YVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEALN 90
+VG L + ++ L D F++ +VV + D + S G+ ++ + +DAA+ ++ L+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKVLD 71
>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 = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 35/47 (74%)
Query: 563 RMLGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
+ LGE+LYP V+ ++P ASK+TGMLLE+ ++L L+ S ++L+ +
Sbjct: 3 QALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRAR 49
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 37/65 (56%), Gaps = 8/65 (12%)
Query: 118 VFIKNLDTSIDNKALCDT-FAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
VFI NL+T++ K+ +T F+ +G V C V KGY FVQ+ NE A+ A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGE 82
Query: 177 NGMLI 181
NG ++
Sbjct: 83 NGRVL 87
>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 = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 27 NVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDA 82
N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V + A
Sbjct: 4 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSA 60
Query: 83 ANAKEALNFMPINGKPIRIMYSHRDPSI 110
NA ++ P KP+RI Y+ D I
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYAKTDSDI 88
Score = 37.4 bits (85), Expect = 0.023, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 312 LYLKNLDDSINDEKLKE----LFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRAL 367
+Y+ NL++ I ++LK+ +FS FG I ++V + +G F F AT AL
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNAL 64
Query: 368 NEMNGKMIGRKPLYVAVAQ 386
M G KP+ + A+
Sbjct: 65 RSMQGFPFYDKPMRIQYAK 83
Score = 36.2 bits (82), Expect = 0.065, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 10/91 (10%)
Query: 209 VYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAV 264
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A+
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 64
Query: 265 EKLNGTTNNDKVWYVGRAQKRAEREADLRAK 295
+ G DK + + A+ ++D+ AK
Sbjct: 65 RSMQGFPFYDKPMRI----QYAKTDSDIIAK 91
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 38/64 (59%), Gaps = 2/64 (3%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKS-RCFGFVNFQSPDAAAAAVEK 266
N+YV NL + T E +K++F FG + + ++ D + K + FGFV Q ++ + A+ K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 267 LNGT 270
L+ T
Sbjct: 62 LDNT 65
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEA-TRALNE 369
N+Y+ NL S E++KELFS+FG + + K++ D+ K GF M EE+ + A+ +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRET-KKPKGFGFVEMQEESVSEAIAK 61
Query: 370 M-NGKMIGR 377
+ N +GR
Sbjct: 62 LDNTDFMGR 70
Score = 36.2 bits (82), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQS-KGYGFVQFENEEAAQNAIKM 175
N+++ NL S ++ + + F+ FG V + K+ D + KG+GFV+ + E ++ K+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL 62
Query: 176 LN 177
N
Sbjct: 63 DN 64
Score = 35.8 bits (81), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
++YVG+L + Q+ +LFSQ +V +V++ D+ + G+ +V + + A
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAK 61
Query: 89 LNFMPINGKPIRIMYSHRDPSI 110
L+ G+ IR+ ++ S+
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSL 83
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 5/82 (6%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAA----AAA 263
+++ L+ T E L++ FG FG + +VM+D +SR FGFV F A +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 264 VEKLNGTTNNDKVWYVGRAQKR 285
+L+ T + KV + RAQ +
Sbjct: 88 RHELDSKTIDPKVAFPRRAQPK 109
Score = 33.1 bits (74), Expect = 0.47, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 5/85 (5%)
Query: 309 GANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRAL 367
G +++ L E L+E F +FG + C VM D S+G GF F + L
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 368 ----NEMNGKMIGRKPLYVAVAQRK 388
+E++ K I K + AQ K
Sbjct: 85 AQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 29.6 bits (65), Expect = 5.3, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENE 166
+FI L + L + F FG V C V D +S+G+GFV F ++
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 49/92 (53%), Gaps = 3/92 (3%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G ++L V +L + L +F + +V V + R+ ++ G+A+V + + +DA +A
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
Query: 86 KEALNFMPINGKPIRIM---YSHRDPSIRKSG 114
+ A++ ++G+ +R+ Y RD S SG
Sbjct: 72 EAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
++V L + ++ED+ ++F FG I V++ DG S+ FV F S A AA+ L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 269 GT 270
G+
Sbjct: 78 GS 79
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 32/61 (52%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L++ L+ ++E + LF FG I C V+ G SKG F FS EA A++ ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 372 G 372
G
Sbjct: 78 G 78
Score = 37.0 bits (84), Expect = 0.031, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 30/61 (49%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+F+ L+ + + F FG + C V +G SKG FV+F + AQ AI L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 178 G 178
G
Sbjct: 78 G 78
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 7/68 (10%)
Query: 202 VSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAA 261
V K ++V NLA TVT+E L+K F FG + +KD + FV+F+ AA
Sbjct: 11 VMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAV 63
Query: 262 AAVEKLNG 269
A++++NG
Sbjct: 64 KAMDEMNG 71
Score = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 46/82 (56%), Gaps = 7/82 (8%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L+++NL ++ +E L++ FSEFG + K + D F F A +A++EMN
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY-------AFVHFEDRGAAVKAMDEMN 70
Query: 372 GKMIGRKPLYVAVAQRKEERKA 393
GK I + + + +A+ +++++
Sbjct: 71 GKEIEGEEIEIVLAKPPDKKRS 92
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+F++NL T++ + L +F+ FG + K + K Y FV FE+ AA A+ +N
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVK-------KLKDYAFVHFEDRGAAVKAMDEMN 70
Query: 178 G 178
G
Sbjct: 71 G 71
>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 = 9e-04, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+FI L S + L + A GTV ++ + G+ KG +V++ENE A A+ ++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 178 GMLINDKQVYVGL 190
GM I + + V +
Sbjct: 80 GMTIKENIIKVAI 92
Score = 36.6 bits (83), Expect = 0.042, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 45/86 (52%), Gaps = 1/86 (1%)
Query: 301 ISRYE-KLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSM 359
+ RY L+ L++ L S E+L+E+ GT+ +++ ++ G KG + +
Sbjct: 8 VFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYEN 67
Query: 360 PEEATRALNEMNGKMIGRKPLYVAVA 385
+A++A+ +M+G I + VA++
Sbjct: 68 ESQASQAVMKMDGMTIKENIIKVAIS 93
Score = 33.9 bits (76), Expect = 0.26, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 38/68 (55%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
++++ L + T E+L++I GT+ ++ + GK + +V +++ A+ AV K++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 269 GTTNNDKV 276
G T + +
Sbjct: 80 GMTIKENI 87
Score = 29.3 bits (64), Expect = 6.8, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++ L + + +L ++ V +R+ +++ + G AYV Y N A+ A +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPK-GLAYVEYENESQASQAVMKM 78
Query: 90 NFMPINGKPIRIMYSHRDPS 109
+ M I I++ S+ PS
Sbjct: 79 DGMTIKENIIKVAISNSGPS 98
>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 = 24/69 (34%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKL 267
++V L+ T ED+K F FG + A++M D + + R FGFV F+S D E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 268 NGTTNNDKV 276
NN V
Sbjct: 62 FHEINNKMV 70
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 194 RQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVN 253
R E SPK VY +A +TD+ +++ F FG I V + + + FV
Sbjct: 13 RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVR 67
Query: 254 FQSPDAAAAAVEKLNGTT 271
F + ++AA A+ +NGTT
Sbjct: 68 FSTHESAAHAIVSVNGTT 85
Score = 36.6 bits (83), Expect = 0.040, Method: Composition-based stats.
Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N ++Y G + + + + FS Q++ +RV ++ GY++V +S + AA+A
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAI 78
Query: 87 EALNFMPINGKPIRIMYSHRDPSI 110
++N I G ++ + P +
Sbjct: 79 VSVNGTTIEGHVVKCYWGKESPDM 102
Score = 35.8 bits (81), Expect = 0.074, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
V+ + + + ++ + TF+ FG ++ +V + KGY FV+F E+A +AI +N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 178 GMLI 181
G I
Sbjct: 83 GTTI 86
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 308 KGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRAL 367
K +Y + + D+ +++ FS FG I +V + KG F FS E A A+
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAI 78
Query: 368 NEMNGKMI 375
+NG I
Sbjct: 79 VSVNGTTI 86
>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 = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 34/45 (75%)
Query: 565 LGEQLYPLVENIEPVHASKVTGMLLEMDQTEVLHLIESPEALKTK 609
LGE+LYP V+ ++P ASK+TGMLLE+ ++L L+ S ++L+ +
Sbjct: 10 LGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRAR 54
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 41/169 (24%), Positives = 71/169 (42%), Gaps = 23/169 (13%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKL 267
N+++ NL + +LK V+ G +R FG+V+F+S + A+E
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELT 74
Query: 268 NGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGA-NLYLKNLDDSINDEKL 326
+++ K E+ + +K++ A L KNL +I +++L
Sbjct: 75 GLKVFGNEI------------------KLEKPKGRDSKKVRAARTLLAKNLSFNITEDEL 116
Query: 327 KELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMNGKMI 375
KE+F + I +V Q G SKG + F +A + L E G I
Sbjct: 117 KEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
Score = 35.8 bits (81), Expect = 0.081, Method: Composition-based stats.
Identities = 36/163 (22%), Positives = 75/163 (46%), Gaps = 16/163 (9%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQV-----AQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAA 83
+L++G+L N + ++L S++ VV VR ++ + YV++ + +D
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK------FGYVDFESAEDLE 68
Query: 84 NAKEALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVL 143
A E L + + G I++ S + + KNL +I L + F L
Sbjct: 69 KALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFE---DAL 124
Query: 144 SCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQV 186
++ + +G+SKG +++F++E A+ ++ G I+ + V
Sbjct: 125 EIRL-VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG-KSRCFGFVNFQSPDAAAAAVEKL 267
+YV LAE V D+ L F FG IT + D + K R F FV F+ + AAAA++ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 268 N 268
N
Sbjct: 126 N 126
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
LYVG L + V++ L+ F + +++ D G+A+V + +DAA A + +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 90 NFMPINGKPIRI 101
N + G+ IR+
Sbjct: 126 NESELFGRTIRV 137
Score = 37.7 bits (86), Expect = 0.018, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
LY+ L + ++D+ L F FG IT ++ +D + +G F F + E+A A++ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 371 N-GKMIGR 377
N ++ GR
Sbjct: 126 NESELFGR 133
Score = 37.0 bits (84), Expect = 0.033, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQS-KGYGFVQFENEEAAQNAIKML 176
+++ L +D+K L F FG + ++ +D + +G+ FV+FE E A AI +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 177 NGMLINDKQVYVGL 190
N + + + V L
Sbjct: 126 NESELFGRTIRVNL 139
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 6/74 (8%)
Query: 197 RAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQ 255
RA N + + V NL+E + DL+++F FG+I+ + KD + G+S+ F F++F
Sbjct: 11 RADDNAT-----IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65
Query: 256 SPDAAAAAVEKLNG 269
+ AA A+ ++G
Sbjct: 66 RREDAARAIAGVSG 79
Score = 37.7 bits (86), Expect = 0.021, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 310 ANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALN 368
A + + NL + + L+ELF FG+I+ + D+ G SKG F +F E+A RA+
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 369 EMNG 372
++G
Sbjct: 76 GVSG 79
Score = 37.4 bits (85), Expect = 0.029, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 108 PSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENE 166
P+ R + + NL L + F FG++ +A D + GQSKG+ F+ F
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 167 EAAQNAIKMLNG 178
E A AI ++G
Sbjct: 68 EDAARAIAGVSG 79
Score = 36.6 bits (83), Expect = 0.039, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 34/59 (57%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
N ++ V +L ++ E+ L +LF + + + +D++ S G+A++++ +DAA A
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 43/76 (56%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G SL V +L + L +F + +V V + RD+ + S G+A+V + + +DA +A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 86 KEALNFMPINGKPIRI 101
+A++ ++G+ +R+
Sbjct: 129 MDAMDGAVLDGRELRV 144
Score = 33.5 bits (75), Expect = 0.40, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFGFVNFQSPDAAAAAVE 265
T++ V+NL + + L+++F +G + + +D K SR F FV F A A++
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 266 KLNG 269
++G
Sbjct: 131 AMDG 134
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 114 GYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNA 172
G ++ + NL L F +G V + D +S+G+ FV+F ++ A++A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 173 IKMLNGMLINDKQVYVGL 190
+ ++G +++ +++ V +
Sbjct: 129 MDAMDGAVLDGRELRVQM 146
Score = 29.3 bits (64), Expect = 7.2, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 311 NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGF-SKGSGFAAFSMPEEATRALNE 369
+L + NL + + L+ +F ++G + + D++ S+G F F +A A++
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 370 MNGKMIGRKPLYVAVAQ 386
M+G ++ + L V +A+
Sbjct: 132 MDGAVLDGRELRVQMAR 148
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKL- 267
++V L+E T+E LK+ F G++ + IV G S+ FGFV+F S + A AA E +
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 268 NGTTNNDKV 276
+G + +KV
Sbjct: 76 DGEIDGNKV 84
Score = 36.2 bits (82), Expect = 0.051, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+L+V L ++ E L + F V R+ D+ SS G+ +V++++ +DA AKEA
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 89 LNFMPINGKPIRIMYS 104
+ I+G + + ++
Sbjct: 74 MEDGEIDGNKVTLDWA 89
Score = 35.4 bits (80), Expect = 0.086, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 108 PSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEE 167
P+ R +F+K L + L ++F G+V + V G SKG+GFV F +EE
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 168 AAQNAIKMLNGMLINDKQV 186
A+ A + + I+ +V
Sbjct: 66 DAKAAKEAMEDGEIDGNKV 84
Score = 33.5 bits (75), Expect = 0.42, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEM- 370
L++K L + +E LKE F G++ + V + G SKG GF F+ E+A A M
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 371 NGKMIGRK 378
+G++ G K
Sbjct: 76 DGEIDGNK 83
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 7/93 (7%)
Query: 22 PSGYGNVSLYVGDLEQNVNESQL----YDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYS 77
P N ++Y+ +L + + + +L + +FS+ Q++ + V R R G A+V +
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXR---GQAFVIFK 57
Query: 78 NPQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
A NA + P KP RI Y+ D I
Sbjct: 58 EVSSATNALRSXQGFPFYDKPXRIQYAKTDSDI 90
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 10/91 (10%)
Query: 209 VYVNNLAETVTDEDLKK----IFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAV 264
+Y+NNL E + ++LKK IF FG I +V + K R FV F+ +A A+
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 66
Query: 265 EKLNGTTNNDKVWYVGRAQKRAEREADLRAK 295
G DK + + A+ ++D+ AK
Sbjct: 67 RSXQGFPFYDKPXRI----QYAKTDSDIIAK 93
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 8/76 (10%)
Query: 192 VRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGK-SRCFG 250
+ R++R ++ +F +++ L+ T+E L+ + +G +T +VM+D K SR FG
Sbjct: 17 LERKKREKE----QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
Query: 251 FVNFQS---PDAAAAA 263
FV F S DAA AA
Sbjct: 73 FVTFSSMAEVDAAMAA 88
>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 = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG-KSRCFGFVNFQSPDAAAAAVEKL 267
+YV LAE V D+ L F FG IT + D + K R F FV F+ + AAAA++ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 268 N 268
N
Sbjct: 65 N 65
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
LYVG L + V++ L+ F + +++ D G+A+V + +DAA A + +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 90 NFMPINGKPIRI 101
N + G+ IR+
Sbjct: 65 NESELFGRTIRV 76
Score = 37.4 bits (85), Expect = 0.026, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
LY+ L + ++D+ L F FG IT ++ +D + +G F F + E+A A++ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 371 N-GKMIGR 377
N ++ GR
Sbjct: 65 NESELFGR 72
Score = 36.6 bits (83), Expect = 0.046, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQS-KGYGFVQFENEEAAQNAIKML 176
+++ L +D+K L F FG + ++ +D + +G+ FV+FE E A AI +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 177 NGMLINDKQVYVGL 190
N + + + V L
Sbjct: 65 NESELFGRTIRVNL 78
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ-SKGYGFVQFENEEAAQNAIKML 176
VFI+NL + +AL + FG + +V + + + SKG F QF +EAAQ +
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 177 N------GMLINDKQVYVGLFVRRQERA 198
+ G+ ++ +Q+ V L V R E A
Sbjct: 78 SLEAEGGGLKLDGRQLKVDLAVTRDEAA 105
Score = 32.3 bits (72), Expect = 0.88, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 308 KGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMV---DQHGFSKGSGFAAFSMPEEAT 364
+G ++++NL +E L E+ +FG + +V++ +H SKG FA F E A
Sbjct: 14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEH--SKGCAFAQFMTQEAAQ 71
Query: 365 RAL 367
+ L
Sbjct: 72 KCL 74
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG-KSRCFGFVNFQSPDAAAAAVEKL 267
+YV LAE V D+ L F FG IT + D + K R F FV F+ + AAAA++ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 268 N 268
N
Sbjct: 68 N 68
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
LYVG L + V++ L+ F + +++ D G+A+V + +DAA A + +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 90 NFMPINGKPIRI 101
N + G+ IR+
Sbjct: 68 NESELFGRTIRV 79
Score = 37.4 bits (85), Expect = 0.028, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
LY+ L + ++D+ L F FG IT ++ +D + +G F F + E+A A++ M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 371 N-GKMIGR 377
N ++ GR
Sbjct: 68 NESELFGR 75
Score = 36.6 bits (83), Expect = 0.048, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQS-KGYGFVQFENEEAAQNAIKML 176
+++ L +D+K L F FG + ++ +D + +G+ FV+FE E A AI +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 177 NGMLINDKQVYVGL 190
N + + + V L
Sbjct: 68 NESELFGRTIRVNL 81
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG-KSRCFGFVNFQSPDAAAAAVEKL 267
+YV LAE V D+ L F FG IT + D + K R F FV F+ + AAAA++ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 268 N 268
N
Sbjct: 70 N 70
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
LYVG L + V++ L+ F + +++ D G+A+V + +DAA A + +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 90 NFMPINGKPIRI 101
N + G+ IR+
Sbjct: 70 NESELFGRTIRV 81
Score = 37.4 bits (85), Expect = 0.028, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
LY+ L + ++D+ L F FG IT ++ +D + +G F F + E+A A++ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 371 N-GKMIGR 377
N ++ GR
Sbjct: 70 NESELFGR 77
Score = 36.6 bits (83), Expect = 0.048, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQS-KGYGFVQFENEEAAQNAIKML 176
+++ L +D+K L F FG + ++ +D + +G+ FV+FE E A AI +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 177 NGMLINDKQVYVGL 190
N + + + V L
Sbjct: 70 NESELFGRTIRVNL 83
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAV 264
++V L + T E L+ F +G + ++MKD + +SR FGFV F+ P+ +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 116 GNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFEN 165
G +F+ LD S + L F+ +G V+ C + D + QS+G+GFV+F++
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Score = 37.0 bits (84), Expect = 0.037, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 28/50 (56%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNP 79
L+VG L+ + + L FSQ +VV + +D++ S G+ +V + +P
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSA-IVMKDSDGKSRCFGFVNFQSPDAAAAAVE 265
+ +Y+ L TD+DL K+ +G I S ++ + K + +GFV+F SP AA AV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 266 KLNGT 270
L +
Sbjct: 66 ALKAS 70
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQN 171
SG ++I+ L ++ L +G ++S K +D + + KGYGFV F++ AAQ
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 172 AIKML 176
A+ L
Sbjct: 63 AVTAL 67
Score = 33.9 bits (76), Expect = 0.31, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 30/64 (46%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G+ LY+ L+ + L L ++VS + D++ GY +V++ +P A A
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 86 KEAL 89
AL
Sbjct: 64 VTAL 67
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDG-KSRCFGFVNFQSPDAAAAAVEKL 267
+YV LAE V D+ L F FG IT + D + K R F FV F+ + AAAA++ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 268 N 268
N
Sbjct: 75 N 75
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
LYVG L + V++ L+ F + +++ D G+A+V + +DAA A + +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSG 114
N + G+ IR+ + + I++SG
Sbjct: 75 NESELFGRTIRVNLA-KPMRIKESG 98
Score = 36.2 bits (82), Expect = 0.052, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
LY+ L + ++D+ L F FG IT ++ +D + +G F F + E+A A++ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 371 N-GKMIGR 377
N ++ GR
Sbjct: 75 NESELFGR 82
Score = 35.8 bits (81), Expect = 0.083, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQS-KGYGFVQFENEEAAQNAIKML 176
+++ L +D+K L F FG + ++ +D + +G+ FV+FE E A AI +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 177 NGMLINDKQVYVGL 190
N + + + V L
Sbjct: 75 NESELFGRTIRVNL 88
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 29/86 (33%), Positives = 50/86 (58%), Gaps = 3/86 (3%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+LYVG+L ++V E + LFSQ+ S ++ + + S+ Y +V + +DAA A A
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAA 74
Query: 89 LNFMPINGKPIRIMYSHRDPSIRKSG 114
+N I GK +++ ++ PS +KSG
Sbjct: 75 MNGRKILGKEVKVNWA-TTPSSQKSG 99
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
LY+ NL + + + +LFS+ G SCK M+ +H + F F +A AL MN
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCK-MITEHTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 372 GKMIGRKPLYVAVAQRKEERKA 393
G+ I K + V A +K+
Sbjct: 77 GRKILGKEVKVNWATTPSSQKS 98
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 7/86 (8%)
Query: 306 KLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATR 365
+L L+++ + + +L E+F FG + K++ G F F E A +
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAK 80
Query: 366 ALNEMNGKMIGRKPLYVAVAQRKEER 391
A+ E++GK +PL V ++ +R
Sbjct: 81 AIEEVHGKSFANQPLEVVYSKLPAKR 106
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
T ++V V + +L +IFG FG + ++ F FV F+ ++AA A+E+
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEE 84
Query: 267 LNGTTNNDKVWYVGRAQKRAER 288
++G + ++ V ++ A+R
Sbjct: 85 VHGKSFANQPLEVVYSKLPAKR 106
Score = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N L+V +V ES+L ++F + V++ G+A+V + + AA A
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAI 82
Query: 87 EALNFMPINGKPIRIMYS 104
E ++ +P+ ++YS
Sbjct: 83 EEVHGKSFANQPLEVVYS 100
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+F++ + L + F FG + K+ G+ FV+FE E+A AI+ ++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVH 86
Query: 178 G 178
G
Sbjct: 87 G 87
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNEM 370
L++ L + +ND+++KEL + FG + + ++ D G SKG F + +A+ +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 371 NGKMIGRKPLYVAVA 385
NG +G K L V A
Sbjct: 64 NGMQLGDKKLLVQRA 78
Score = 38.5 bits (88), Expect = 0.012, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+FI L +++ + + +FG + + + DS G SKGY F ++ + AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 177 NGMLINDKQVYV 188
NGM + DK++ V
Sbjct: 64 NGMQLGDKKLLV 75
Score = 33.9 bits (76), Expect = 0.31, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKL 267
+++ L + D+ +K++ FG + + ++KDS G S+ + F + + A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 268 NGTTNNDKVWYVGRAQKRAE 287
NG DK V RA A+
Sbjct: 64 NGMQLGDKKLLVQRASVGAK 83
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 34/72 (47%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L++G L +N+ Q+ +L + + + + +D + S GYA+ Y + A L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 90 NFMPINGKPIRI 101
N M + K + +
Sbjct: 64 NGMQLGDKKLLV 75
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNF 254
+++ L+ T E L++ FG FG + +VM+D +SR FGFV F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 30.4 bits (67), Expect = 2.8, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAF 357
+++ L E L+E F +FG + C VM D S+G GF F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENE 166
+FI L + L + F FG V C V D +S+G+GFV F ++
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 37/72 (51%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V + + E ++ + F ++ ++ + D+ S GYA V Y + A AKEAL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 90 NFMPINGKPIRI 101
N I G+ I++
Sbjct: 89 NGAEIMGQTIQV 100
Score = 33.9 bits (76), Expect = 0.30, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 307 LKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATR 365
++G L++ ++ + +++++E F ++G I + + +D+ GFSKG + ++A
Sbjct: 24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 83
Query: 366 ALNEMNGKMI 375
A +NG I
Sbjct: 84 AKEALNGAEI 93
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F+ ++ + + F +G + + + +D G SKGY V++E + A A + L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 177 NGMLINDKQVYVG-LFVRRQER 197
NG I + + V FV+ +R
Sbjct: 89 NGAEIMGQTIQVDWCFVKGPKR 110
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
L L NL S +E L+E+F + T KV +Q+G SKG F F+ E+A ALN N
Sbjct: 18 LVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 372 GKMI 375
+ I
Sbjct: 75 KREI 78
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 118 VFIKNLDTSIDNKALCDTF--AAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKM 175
+ + NL S + L + F A F KV + NG+SKGY F++F + E A+ A+
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATF-----IKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 176 LNGMLINDKQVYVGL 190
N I + + + L
Sbjct: 73 CNKREIEGRAIRLEL 87
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
+L + +L + E L ++F + ++V ++Q+ +S GYA++ +++ +DA A +
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKA---TFIKVPQNQNGKSK-GYAFIEFASFEDAKEALNS 72
Query: 89 LNFMPINGKPIRI 101
N I G+ IR+
Sbjct: 73 CNKREIEGRAIRL 85
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+F+ N+ + ++ L F G V+ C V K Y FV E E A+ AI LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLN 64
Query: 178 GMLINDKQVYVGLFVRRQERA 198
G + K++ V L + Q+++
Sbjct: 65 GKEVKGKRINVELSTKGQKKS 85
Score = 32.7 bits (73), Expect = 0.67, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
++V N++ T ++L+ +F G + V+KD + FV+ + A AA+ +LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 269 G 269
G
Sbjct: 65 G 65
Score = 30.8 bits (68), Expect = 2.2, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
++VG++ +L LF + +V+ V +D YA+V+ DA A L
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 90 NFMPINGKPIRIMYSHRDPSIRKSG 114
N + GK I + S + +KSG
Sbjct: 64 NGKEVKGKRINVELSTKGQ--KKSG 86
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 39/168 (23%), Positives = 66/168 (39%), Gaps = 21/168 (12%)
Query: 208 NVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKL 267
N++V NL + +LK V+ G +R FG+V+F+S + A+E
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALELT 68
Query: 268 NGTTNNDKVWYVGRAQKRAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKLK 327
+++ K +++E D R L KNL + ++LK
Sbjct: 69 GLKVFGNEIKLEKPKGKDSKKERDAR-----------------TLLAKNLPYKVTQDELK 111
Query: 328 ELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMNGKMI 375
E+F + I +V + G SKG + F +A + E G I
Sbjct: 112 EVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 35/163 (21%), Positives = 69/163 (42%), Gaps = 16/163 (9%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQV-----AQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAA 83
+L+VG+L N + +L S V VV VR+ + + YV++ + +D
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRK------FGYVDFESAEDLE 62
Query: 84 NAKEALNFMPINGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVL 143
A E L + + G I++ S ++ + KNL + L + F +
Sbjct: 63 KALE-LTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIR 121
Query: 144 SCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQV 186
+ +G+SKG +++F+ E A+ + G I+ + +
Sbjct: 122 ----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 306 KLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATR 365
+L L+++ + + +L E+F FG + K++ G F F E A +
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAK 53
Query: 366 ALNEMNGKMIGRKPLYVAVAQ 386
A+ E++GK +PL V ++
Sbjct: 54 AIEEVHGKSFANQPLEVVYSK 74
Score = 35.4 bits (80), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 7/65 (10%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
T ++V V + +L +IFG FG + ++ F FV F+ ++AA A+E+
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEE 57
Query: 267 LNGTT 271
++G +
Sbjct: 58 VHGKS 62
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
N L+V +V ES+L ++F + V++ G+A+V + + AA A
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKA 54
Query: 86 KEALNFMPINGKPIRIMYS 104
E ++ +P+ ++YS
Sbjct: 55 IEEVHGKSFANQPLEVVYS 73
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+F++ + L + F FG + K+ G+ FV+FE E+A AI+ ++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVH 59
Query: 178 G 178
G
Sbjct: 60 G 60
>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 = 38.9 bits (89), Expect = 0.009, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 37/72 (51%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V + + E ++ + F ++ ++ + D+ S GYA V Y + A AKEAL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 90 NFMPINGKPIRI 101
N I G+ I++
Sbjct: 135 NGAEIMGQTIQV 146
Score = 33.1 bits (74), Expect = 0.47, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 307 LKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATR 365
++G L++ ++ + +++++E F ++G I + + +D+ GFSKG + ++A
Sbjct: 70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129
Query: 366 ALNEMNGKMI 375
A +NG I
Sbjct: 130 AKEALNGAEI 139
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F+ ++ + + F +G + + + +D G SKGY V++E + A A + L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 177 NGMLINDKQVYVG-LFVRRQERAQQN 201
NG I + + V FV+ +R +++
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVKKS 160
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
+Y+G + + E Q+ DL S V V+++++ D S GYA++ + + + +A+A L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 90 NFMPINGKPIRIMYS 104
N + + ++ YS
Sbjct: 65 NGYQLGSRFLKCGYS 79
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKML 176
V++ ++ + + D + G V++ K+ D G+SKGY F++F + E++ +A++ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 177 NGMLINDKQVYVG 189
NG + + + G
Sbjct: 65 NGYQLGSRFLKCG 77
Score = 36.2 bits (82), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
+YL ++ +E++ +L S G + + K+M D Q G SKG F F E + A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 371 NGKMIGRKPL 380
NG +G + L
Sbjct: 65 NGYQLGSRFL 74
Score = 33.9 bits (76), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKL 267
VY+ ++ T+E + + + G + + +M D G+S+ + F+ F+ +++A+AV L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 268 NG 269
NG
Sbjct: 65 NG 66
>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 = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
+Y+G + + E Q+ DL S V V+++++ D S GYA++ + + + +A+A L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 90 NFMPINGKPIRIMYS 104
N + + ++ YS
Sbjct: 67 NGYQLGSRFLKCGYS 81
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKML 176
V++ ++ + + D + G V++ K+ D G+SKGY F++F + E++ +A++ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 177 NGMLINDKQVYVG 189
NG + + + G
Sbjct: 67 NGYQLGSRFLKCG 79
Score = 36.2 bits (82), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
+YL ++ +E++ +L S G + + K+M D Q G SKG F F E + A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 371 NGKMIGRKPL 380
NG +G + L
Sbjct: 67 NGYQLGSRFL 76
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKL 267
VY+ ++ T+E + + + G + + +M D G+S+ + F+ F+ +++A+AV L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 268 NG 269
NG
Sbjct: 67 NG 68
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
+Y+G + + E Q+ DL S V V+++++ D S GYA++ + + + +A+A L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 90 NFMPINGKPIRIMYS 104
N + + ++ YS
Sbjct: 66 NGYQLGSRFLKCGYS 80
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIKML 176
V++ ++ + + D + G V++ K+ D G+SKGY F++F + E++ +A++ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 177 NGMLINDKQVYVG 189
NG + + + G
Sbjct: 66 NGYQLGSRFLKCG 78
Score = 36.2 bits (82), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
+YL ++ +E++ +L S G + + K+M D Q G SKG F F E + A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 371 NGKMIGRKPL 380
NG +G + L
Sbjct: 66 NGYQLGSRFL 75
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNFQSPDAAAAAVEKL 267
VY+ ++ T+E + + + G + + +M D G+S+ + F+ F+ +++A+AV L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 268 NG 269
NG
Sbjct: 66 NG 67
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 118 VFIKNLDTSIDNKALCDT-FAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKML 176
VFI NL+T + K+ + F+ +G ++ C V KG+ FVQ+ NE A+ A+
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGE 70
Query: 177 NGMLI 181
+G +I
Sbjct: 71 DGRMI 75
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 5/60 (8%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
T +YV L +T+T+ DL+ F FG I + V++ + +C F+ F + AA A EK
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ----RQQC-AFIQFATRQAAEVAAEK 67
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.7 bits (86), Expect = 0.017, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 307 LKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHG--FSKGSGFAAFSMPEEAT 364
+K +++ L ++ + + E+FS +G I + V++ SKG + F P+EA
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 365 RALNEMNGKMI 375
+AL M+G I
Sbjct: 62 KALKHMDGGQI 72
Score = 36.2 bits (82), Expect = 0.062, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQ-SKRSSLGYAYVNYSNPQDAANAKEA 88
+++G L +NV + + ++FS ++ + + ++ S GYAYV + NP +A A +
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 89 LNFMPINGKPI 99
++ I+G+ I
Sbjct: 67 MDGGQIDGQEI 77
Score = 35.8 bits (81), Expect = 0.071, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQ--SKGYGFVQFENEEAAQNAIKM 175
V I L ++ + + F+ +G + + ++ SKGY +V+FEN + A+ A+K
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 176 LNGMLINDKQV 186
++G I+ +++
Sbjct: 67 MDGGQIDGQEI 77
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 7/88 (7%)
Query: 27 NVSLYVGDLEQNVNES----QLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDA 82
N ++Y+ +L + + + LY +FSQ Q++ + + R G A+V + A
Sbjct: 6 NQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMR---GQAFVIFKEIGSA 62
Query: 83 ANAKEALNFMPINGKPIRIMYSHRDPSI 110
+NA + P KP++I YS D I
Sbjct: 63 SNALRTMQGFPFYDKPMQIAYSKSDSDI 90
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 6/95 (6%)
Query: 208 NVYVNNL----AETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
+Y+NNL + + L IF FG I + +K K R FV F+ +A+ A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTL--KMRGQAFVIFKEIGSASNA 65
Query: 264 VEKLNGTTNNDKVWYVGRAQKRAEREADLRAKFEQ 298
+ + G DK + ++ ++ A ++ F++
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKE 100
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 6/101 (5%)
Query: 305 EKLKGANLYLKNLDDSINDE----KLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMP 360
E L +Y+ NL++ I E L +FS+FG I + +G F F
Sbjct: 2 EMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVIFKEI 59
Query: 361 EEATRALNEMNGKMIGRKPLYVAVAQRKEERKARLQAQFAQ 401
A+ AL M G KP+ +A ++ + A+++ F +
Sbjct: 60 GSASNALRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKE 100
>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 = 37.7 bits (86), Expect = 0.019, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V + + E ++D F++ ++ ++ + D+ GY V Y ++A A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 90 NFMPINGKPIRI 101
N + G+PI +
Sbjct: 70 NGQDLMGQPISV 81
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 307 LKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATR 365
++G L++ + + +E + + F+E+G I + + +D+ G+ KG + +EA
Sbjct: 5 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 64
Query: 366 ALNEMNGKMIGRKPLYV 382
A+ +NG+ + +P+ V
Sbjct: 65 AMEGLNGQDLMGQPISV 81
Score = 34.3 bits (77), Expect = 0.22, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F+ + + + D FA +G + + + +D G KGY V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NG 178
NG
Sbjct: 70 NG 71
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 37.7 bits (86), Expect = 0.020, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 113 SGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNA 172
SG +FI NL + + F +G VL C + K YGFV E++ AA++A
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58
Query: 173 IKMLN 177
I+ L+
Sbjct: 59 IRNLH 63
Score = 29.3 bits (64), Expect = 7.9, Method: Composition-based stats.
Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
G V L++G+L + E ++ LF Q +V+ + ++ Y +V+ + A +A
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDA 58
Query: 86 KEALNFMPINGKPIRIMYS 104
L+ ++G I + S
Sbjct: 59 IRNLHHYKLHGVNINVEAS 77
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 10/74 (13%)
Query: 30 LYVGDLEQNVNESQLYDLFSQV--AQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKE 87
LYV +L + +E + F+ + V V+ RD YA+V++SN +DA A +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMK 69
Query: 88 ALNFMPINGKPIRI 101
ALN ++G PI +
Sbjct: 70 ALNGKVLDGSPIEV 83
Score = 33.1 bits (74), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 312 LYLKNLDDSINDEKLKELFSEF--GTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNE 369
LY++NL S ++E +++ F+ G + K + D F FS E+A A+
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDY-------AFVHFSNREDAVEAMKA 70
Query: 370 MNGKMIGRKPLYVAVAQ 386
+NGK++ P+ V +A+
Sbjct: 71 LNGKVLDGSPIEVTLAK 87
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 148 AIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGL 190
A++ + + Y FV F N E A A+K LNG +++ + V L
Sbjct: 43 AVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL 85
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 37.7 bits (86), Expect = 0.022, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V + + E ++D F++ ++ ++ + D+ GY V Y ++A A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 90 NFMPINGKPIRI 101
N + G+PI +
Sbjct: 70 NGQDLMGQPISV 81
Score = 33.9 bits (76), Expect = 0.25, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F+ + + + D FA +G + + + +D G KGY V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NGMLINDKQVYVG-LFVR 193
NG + + + V FVR
Sbjct: 70 NGQDLMGQPISVDWCFVR 87
>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 = 37.4 bits (85), Expect = 0.024, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V + + E ++D F++ ++ ++ + D+ GY V Y ++A A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 90 NFMPINGKPIRI 101
N + G+PI +
Sbjct: 70 NGQDLMGQPISV 81
Score = 33.9 bits (76), Expect = 0.27, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F+ + + + D FA +G + + + +D G KGY V++E + AQ A++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NGMLINDKQVYVG-LFVR 193
NG + + + V FVR
Sbjct: 70 NGQDLMGQPISVDWCFVR 87
>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 = 37.4 bits (85), Expect = 0.024, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V + + E ++D F++ ++ ++ + D+ GY V Y ++A A E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 90 NFMPINGKPIRI 101
N + G+PI +
Sbjct: 72 NGQDLMGQPISV 83
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F+ + + + D FA +G + + + +D G KGY V++E + AQ A++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 177 NGMLINDKQVYVG-LFVR 193
NG + + + V FVR
Sbjct: 72 NGQDLMGQPISVDWCFVR 89
>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 = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V + + E ++D F++ ++ ++ + D+ GY V Y ++A A E L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 90 NFMPINGKPIRI 101
N + G+PI +
Sbjct: 85 NGQDLMGQPISV 96
Score = 34.3 bits (77), Expect = 0.24, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 307 LKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATR 365
++G L++ + + +E + + F+E+G I + + +D+ G+ KG + +EA
Sbjct: 20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 79
Query: 366 ALNEMNGKMIGRKPLYV 382
A+ +NG+ + +P+ V
Sbjct: 80 AMEGLNGQDLMGQPISV 96
Score = 33.9 bits (76), Expect = 0.31, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F+ + + + D FA +G + + + +D G KGY V++E + AQ A++ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 177 NG 178
NG
Sbjct: 85 NG 86
>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 = 37.0 bits (84), Expect = 0.033, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+V + + E ++D F++ ++ ++ + D+ GY V Y ++A A E L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 90 NFMPINGKPIRI 101
N + G+PI +
Sbjct: 86 NGQDLMGQPISV 97
Score = 33.5 bits (75), Expect = 0.38, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKML 176
+F+ + + + D FA +G + + + +D G KGY V++E + AQ A++ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 177 NG 178
NG
Sbjct: 86 NG 87
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 37.0 bits (84), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N LY+ +L + ++YD+F + + +RV R G AYV Y + DA NA
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAV 64
Query: 87 EALNFMPINGKPIRIMYSHRDPSIRK 112
+ L+ ++ + + ++Y + + + +K
Sbjct: 65 DHLSGFNVSNRYLVVLYYNANRAFQK 90
Score = 36.2 bits (82), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 46/88 (52%), Gaps = 4/88 (4%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
++I+NL I + + D F +G + +V + +++G +V +E+ A+NA+ L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSPK 205
G ++++ Y+ + RA Q + K
Sbjct: 69 GFNVSNR--YLVVLYYNANRAFQKMDTK 94
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 48/96 (50%), Gaps = 3/96 (3%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
+Y+ NL +T E++ IFG +G I V + ++R +V ++ A AV+ L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 269 G-TTNNDKVWYVGRAQKRAEREADLRAKFEQERISR 303
G +N + + RA ++ D + K EQ ++ +
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLK 104
Score = 29.3 bits (64), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEATRALNEMN 371
LY++NL I E++ ++F ++G I + V ++G+ + + +A A++ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIR--VGNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 372 GKMIGRKPLYV 382
G + + L V
Sbjct: 69 GFNVSNRYLVV 79
>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 = 36.6 bits (83), Expect = 0.041, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 30 LYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEAL 89
L+VG+L ++ E ++ LF + + V + +D+ G+ ++ A AK L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVEL 71
Query: 90 NFMPINGKPIRIMYSHRDPSI 110
+ MP+ GK +R+ ++ S+
Sbjct: 72 DNMPLRGKQLRVRFACHSASL 92
Score = 32.3 bits (72), Expect = 0.77, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
+ ++V NL +T+E+++K+F +G + KD + FGF+ ++ A A +
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVE 70
Query: 267 LN 268
L+
Sbjct: 71 LD 72
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKR--SSLGYAYVNYSNPQDAANA 85
+ ++VG + + +E L +LF Q V + V RD+S+ S G +V + + A A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 86 KEALNFM--------PINGKP 98
+ AL+ M PI KP
Sbjct: 64 QNALHNMKVLPGMHHPIQMKP 84
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.2 bits (82), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 312 LYLKNLDDSINDEKLKELFSEF----GTITSCKVMVDQHGFSKGSGFAAFSMPEEATRAL 367
LYLKNL + + L LF+ F G ++M G +G F F E A +AL
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT---GRMRGQAFITFPNKEIAWQAL 84
Query: 368 NEMNGKMIGRKPLYVAVAQRKEERKA 393
+ +NG + K L + + K++R +
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSS 110
Score = 35.8 bits (81), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 42/85 (49%), Gaps = 7/85 (8%)
Query: 118 VFIKNLDTSIDNKALCDTFAAF----GTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAI 173
+++KNL + + L FA F G + ++ G+ +G F+ F N+E A A+
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQAL 84
Query: 174 KMLNGMLINDKQVYVGLFVRRQERA 198
++NG + K + + +++R+
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRS 109
Score = 33.5 bits (75), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 1/83 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITS-AIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKL 267
+Y+ NL+ VT+ DL +F F I + G+ R F+ F + + A A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 268 NGTTNNDKVWYVGRAQKRAEREA 290
NG K+ + + + +R +
Sbjct: 88 NGYKLYGKILVIEFGKNKKQRSS 110
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 36.2 bits (82), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 38/191 (19%), Positives = 72/191 (37%), Gaps = 37/191 (19%)
Query: 108 PSIRKSGYGNVFIKNLDTS-IDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENE 166
P + +G + + NL+ + ++L F +G V K+ + K VQ +
Sbjct: 27 PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADG 82
Query: 167 EAAQNAIKMLNGMLINDKQVYVGL-----------------------------FVRRQER 197
AQ A+ LNG ++ K + + L F + +
Sbjct: 83 NQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSK 142
Query: 198 AQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSP 257
QN+ P ++++N+ +V++EDLK +F G + D R + S
Sbjct: 143 NFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSV 199
Query: 258 DAAAAAVEKLN 268
+ A A+ L+
Sbjct: 200 EEAVQALIDLH 210
Score = 32.0 bits (71), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 7/94 (7%)
Query: 23 SGYGNVSLYVGDLE-QNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQD 81
+G GN L V +L + V L+ LF V V++ ++ + A V ++
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQ 84
Query: 82 AANAKEALNFMPINGKPIRIMYS-HRDPSIRKSG 114
A A LN ++GKPIRI S H++ + + G
Sbjct: 85 AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREG 118
>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 = 35.8 bits (81), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 47 LFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA-LNFMPINGKPIRIMYSH 105
L S Q VR+ R++S S G+A+V +S+ QDA EA + + I G+ + + YS
Sbjct: 22 LQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD 81
Query: 106 RDPSI 110
P I
Sbjct: 82 PKPKI 86
>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 = 35.8 bits (81), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 3/86 (3%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N LY+ +L + ++YD+F + + +RV R G AYV Y + DA NA
Sbjct: 18 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAC 74
Query: 87 EALNFMPINGKPIRIMYSHRDPSIRK 112
+ L+ + + + ++Y + + + +K
Sbjct: 75 DHLSGFNVCNRYLVVLYYNANRAFQK 100
Score = 32.7 bits (73), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 4/88 (4%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
++I+NL I + + D F +G + +V + +++G +V +E+ A+NA L+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSPK 205
G + ++ Y+ + RA Q + K
Sbjct: 79 GFNVCNR--YLVVLYYNANRAFQKMDTK 104
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 51/108 (47%), Gaps = 4/108 (3%)
Query: 196 ERAQQNVSPKFTNV-YVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNF 254
+RA + P+ + Y+ NL +T E++ IFG +G I V + ++R +V +
Sbjct: 7 KRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVY 64
Query: 255 QSPDAAAAAVEKLNG-TTNNDKVWYVGRAQKRAEREADLRAKFEQERI 301
+ A A + L+G N + + RA ++ D + K EQ ++
Sbjct: 65 EDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKL 112
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 22/98 (22%), Positives = 47/98 (47%), Gaps = 12/98 (12%)
Query: 285 RAEREADLRAKFEQERISRYEKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVD 344
+A + A++R E RI LY++NL I E++ ++F ++G I ++ V
Sbjct: 4 QAAKRANIRLPPEVNRI----------LYIRNLPYKITAEEMYDIFGKYGPIR--QIRVG 51
Query: 345 QHGFSKGSGFAAFSMPEEATRALNEMNGKMIGRKPLYV 382
++G+ + + +A A + ++G + + L V
Sbjct: 52 NTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVV 89
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.8 bits (81), Expect = 0.069, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N LY+ +L + ++YD+F + + +RV R G AYV Y + DA NA
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAC 68
Query: 87 EALNFMPINGKPIRIMY 103
+ L+ + + + ++Y
Sbjct: 69 DHLSGFNVCNRYLVVLY 85
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
++I+NL I + + D F +G + +V + +++G +V +E+ A+NA L+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNACDHLS 72
Query: 178 GMLINDKQVYV 188
G + ++ + V
Sbjct: 73 GFNVCNRYLVV 83
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 35.4 bits (80), Expect = 0.091, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVEKLN 268
VYV NL +L++ F ++G + + + ++ G F FV F+ P A AV L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 58
Query: 269 G 269
G
Sbjct: 59 G 59
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 28 VSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKE 87
+ +YVG+L + +L FS + +V + R+ G+A+V + +P+DA +A
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVR 55
Query: 88 ALNFMPINGKPIRIMYSHRDP 108
L+ I G +R+ S P
Sbjct: 56 GLDGKVICGSRVRVELSTGMP 76
Score = 34.7 bits (78), Expect = 0.16, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
V++ NL T L F+ +G + + +A + G+ FV+FE+ A++A++ L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP----PGFAFVEFEDPRDAEDAVRGLD 58
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSP 204
G +I +V V L R++ + P
Sbjct: 59 GKVICGSRVRVELSTGMPRRSRFDRPP 85
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQ 80
+++ L + L D FS V +V VR+ D++ R S G AYV + Q
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNG-QSKGYGFVQFENEEAAQNAIKM 175
VF L I + L D F+A G V ++ D N +SKG +V+F ++ AI +
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 86
Query: 176 LNGMLI 181
L+
Sbjct: 87 TGQRLL 92
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVL-SCKVAIDSNGQSKGYGFVQFENEEAAQNAI 173
V++K L +NK + D F V S +A NG++ G GFV+F NE + A+
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 84
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 21/95 (22%), Positives = 48/95 (50%), Gaps = 6/95 (6%)
Query: 22 PSGYGNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQD 81
P+G + +YVG+L ++ + D+F + + + + +++R +A+V + +P+D
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRD 73
Query: 82 AANAKEALNFMPINGKPIRIMYSHRDPSIRKSGYG 116
A +A + +G +R+ + S R +G G
Sbjct: 74 AEDAVYGRDGYDYDGYRLRVEFPR---SGRGTGSG 105
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQS-KGYGFVQFENEEAAQNAIKM 175
+F+ + + L + F FG V + D+ Q +G+GF+ FE+E++ A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRALNEM 370
+++ + + + +L+E F +FG +T ++ D + +G GF F + +A+N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 371 NGKMIGRK 378
++G+K
Sbjct: 73 FHDIMGKK 80
>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 = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 48/97 (49%), Gaps = 6/97 (6%)
Query: 95 NGKPIRIMYSHRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGT--VLSCKVAID-S 151
N K I+Y++ R++ V++ + ++ L + G V+ K A + +
Sbjct: 38 NNKTPAILYTYSGLRNRRAA---VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94
Query: 152 NGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
NGQSKGY V +E + +++L G ++N ++V V
Sbjct: 95 NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDV 131
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 9/67 (13%)
Query: 200 QNVSPKFTNVYVNNLA-ETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPD 258
N+ PK + +++ NL + V+ EDL +IF +G I I +K++ FGF+ F +P
Sbjct: 5 HNIPPK-SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQ-INIKNA------FGFIQFDNPQ 56
Query: 259 AAAAAVE 265
+ A+E
Sbjct: 57 SVRDAIE 63
Score = 28.9 bits (63), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 11/70 (15%)
Query: 105 HRDPSIRKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFE 164
H P + GN+ +KN + + L F+ +G ++ + +GF+QF+
Sbjct: 5 HNIPPKSRLFIGNLPLKN----VSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFD 53
Query: 165 NEEAAQNAIK 174
N ++ ++AI+
Sbjct: 54 NPQSVRDAIE 63
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 34.3 bits (77), Expect = 0.24, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 205 KFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKD-SDGKSRCFGFVNF 254
K +++ V L T++DLK+ F FG + V KD G S+ FGFV F
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Score = 33.1 bits (74), Expect = 0.49, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 308 KGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVD-QHGFSKGSGFAAFSMPEEATRA 366
K ++L + L ++ LKE FS FG + +V D + G SKG GF F+ E +
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 367 LNE 369
+++
Sbjct: 74 MSQ 76
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 132 LCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEE 167
L + F+ FG VL +V D G SKG+GFV+F E
Sbjct: 32 LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 33.5 bits (75), Expect = 0.37, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQH-GFSKGSGFAAFSMPEEATRALNEM 370
L++ + +++++ LK LF EFG I V+ D+ G KG F + E A +A + +
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 371 N 371
+
Sbjct: 76 H 76
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 33.1 bits (74), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 203 SPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAA 262
S +Y+ NL+ VT +DL+++FG + V+ S + FV++ + A
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----GYAFVDYPDQNWAIR 59
Query: 263 AVEKLNG 269
A+E L+G
Sbjct: 60 AIETLSG 66
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 32.7 bits (73), Expect = 0.57, Method: Composition-based stats.
Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 305 EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKV--MVDQHGFSKGSGFAAFSMPEE 362
+K + + ++N+ N +++ELFS FG + + ++ + G +G GF F ++
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 363 ATRALNEM 370
A +A N +
Sbjct: 71 AKKAFNAL 78
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 14/68 (20%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 111 RKSGYGNVFIKNLDTSIDNKALCDTFAAFGTVLSCKV--AIDSNGQSKGYGFVQFENEEA 168
+K + ++N+ + + + + F+ FG + + ++ + G +G+GFV F ++
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 169 AQNAIKML 176
A+ A L
Sbjct: 71 AKKAFNAL 78
Score = 29.3 bits (64), Expect = 6.6, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 21 VPSGYGNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSS-LGYAYVNYSNP 79
VP + V ++ N+ ++ +LFS ++ +VR+ + + + G+ +V++
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 80 QDAANAKEAL 89
QDA A AL
Sbjct: 69 QDAKKAFNAL 78
>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 = 32.7 bits (73), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 3/86 (3%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAK 86
N L + +L + ++YD+F + + +RV R G AYV Y + DA NA
Sbjct: 18 NRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAC 74
Query: 87 EALNFMPINGKPIRIMYSHRDPSIRK 112
+ L+ + + + ++Y + + + +K
Sbjct: 75 DHLSGFNVCNRYLVVLYYNANRAFQK 100
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
+ I+NL I + + D F +G + +V + +++G +V +E+ A+NA L+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSPK 205
G + ++ Y+ + RA Q + K
Sbjct: 79 GFNVCNR--YLVVLYYNANRAFQKMDTK 104
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 32.7 bits (73), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 37/185 (20%), Positives = 69/185 (37%), Gaps = 37/185 (20%)
Query: 114 GYGNVFIKNLDTS-IDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNA 172
G + + NL+ + ++L F +G V K+ + K VQ + AQ A
Sbjct: 2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLA 57
Query: 173 IKMLNGMLINDKQVYVGL-----------------------------FVRRQERAQQNVS 203
+ LNG ++ K + + L F + + QN+
Sbjct: 58 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117
Query: 204 PKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAA 263
P ++++N+ +V++EDLK +F G + D R + S + A A
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQA 174
Query: 264 VEKLN 268
+ L+
Sbjct: 175 LIDLH 179
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 7/91 (7%)
Query: 26 GNVSLYVGDLE-QNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAAN 84
GN L V +L + V L+ LF V V++ ++ + A V ++ A
Sbjct: 2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQL 56
Query: 85 AKEALNFMPINGKPIRIMYS-HRDPSIRKSG 114
A LN ++GKPIRI S H++ + + G
Sbjct: 57 AMSHLNGHKLHGKPIRITLSKHQNVQLPREG 87
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 32.7 bits (73), Expect = 0.69, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 305 EKLKGA-NLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKGSGFAAFSMPEEA 363
+K++ A L KNL +I +++LKE+F + I +V Q G SKG + F +A
Sbjct: 11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADA 66
Query: 364 TRALNEMNGKMI 375
+ L E G I
Sbjct: 67 EKNLEEKQGAEI 78
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.7 bits (73), Expect = 0.71, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITS-AIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
++V L+ +E +++ FG FG + S + M + K R F F+ F+ + +EK
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 = 32.3 bits (72), Expect = 0.74, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITS-AIVMKDSDGKSRCFGFVNFQSPDAAAAAVEK 266
++V L+ +E +++ FG FG + S + M + K R F F+ F+ + +EK
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|3C9Z|A Chain A, Sambucus Nigra Agglutinin Ii (Sna-Ii), Tetragonal Crystal
Form
pdb|3CA0|A Chain A, Sambucus Nigra Agglutinin Ii (Sna-Ii), Hexagonal Crystal
Form
pdb|3CA1|A Chain A, Sambucus Nigra Agglutinin Ii (Sna-Ii)- Tetragonal Crystal
Form- Complexed To Galactose
pdb|3CA3|A Chain A, Crystal Structure Of Sambucus Nigra Agglutinin Ii
(Sna-Ii)-Tetragonal Crystal Form- Complexed To
N-Acetylgalactosamine
pdb|3CA4|A Chain A, Sambucus Nigra Agglutinin Ii, Tetragonal Crystal Form-
Complexed To Lactose
pdb|3CA5|A Chain A, Crystal Structure Of Sambucus Nigra Agglutinin Ii
(Sna-Ii)-Tetragonal Crystal Form- Complexed To Alpha1
Methylgalactose
pdb|3CAH|A Chain A, Sambucus Nigra Aggutinin Ii. Tetragonal Crystal Form-
Complexed To Fucose
pdb|3CA6|A Chain A, Sambucus Nigra Agglutinin Ii (Sna-Ii)- Tetragonal Crystal
Form- Complexed To Tn Antigen
Length = 258
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 6/89 (6%)
Query: 135 TFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKM---LNGMLINDKQVYVGLF 191
TF + T+ S + +NG + G V F AA+NAIK ++G +IN GL
Sbjct: 42 TFDSDDTIRSMGKCMTANGLNNGSNIVIFNCSTAAENAIKWEVPIDGSIINPSS---GLV 98
Query: 192 VRRQERAQQNVSPKFTNVYVNNLAETVTD 220
+ A + + N+Y + TVT+
Sbjct: 99 MTAPRAASRTILLLEDNIYAASQGWTVTN 127
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 207 TNVYVNNLAETVTDEDLKKIFGHFGTITS 235
+YV NLA+ V ++DLK IFG + +S
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSS 74
>pdb|1IFW|A Chain A, Solution Structure Of C-Terminal Domain Of Poly(A) Binding
Protein From Saccharomyces Cerevisiae
Length = 92
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 563 RMLGEQLYPLV--ENIEPVHASKVTGMLLEMDQTEVLHLIESPE 604
+ LGEQLY V + A K+TGM+L++ EV L+ES E
Sbjct: 22 QALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDE 65
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 8/60 (13%)
Query: 207 TNVYVNNL-AETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVE 265
+ +++ NL + V+ EDL +IF +G I I +K++ FGF+ F +P + A+E
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQ-INIKNA------FGFIQFDNPQSVRDAIE 75
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQ-HGFSKGSGFAAFSMPEEATRALNEM 370
L++ + ++++ LK LF EFG I V+ D+ G KG F + + A +A + +
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 371 N 371
+
Sbjct: 78 H 78
Score = 28.9 bits (63), Expect = 9.9, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITSAIVMKDS-DGKSRCFGFVNFQSPDAAAAAVEKL 267
++V + + ++DLK +F FG I V+KD G + F+ + + D+A A L
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 268 N 268
+
Sbjct: 78 H 78
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 8/60 (13%)
Query: 207 TNVYVNNL-AETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAAAVE 265
+ +++ NL + V+ EDL +IF +G I I +K++ FGF+ F +P + A+E
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQ-INIKNA------FGFIQFDNPQSVRDAIE 75
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 9/70 (12%)
Query: 209 VYVNNLAETVTDEDLKKIFGHFGTITS---------AIVMKDSDGKSRCFGFVNFQSPDA 259
+YV L ++VT +DL F G + I + GK + V+++ P
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 260 AAAAVEKLNG 269
A AAVE +G
Sbjct: 78 AKAAVEWFDG 87
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 9/86 (10%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCK--------VMVDQH-GFSKGSGFAAFSMPEE 362
+Y++ L+DS+ + L + F + G + K + +D+ G KG ++ P
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 363 ATRALNEMNGKMIGRKPLYVAVAQRK 388
A A+ +GK L V++A++K
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 8/92 (8%)
Query: 27 NVSLYVGDLEQNVNESQLYDLFSQVAQV--------VSVRVCRDQSKRSSLGYAYVNYSN 78
N ++YV L +V L D F Q V + + D+ G A V+Y +
Sbjct: 15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 79 PQDAANAKEALNFMPINGKPIRIMYSHRDPSI 110
P A A E + G +++ + + P +
Sbjct: 75 PPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 9/63 (14%)
Query: 204 PKFTNVYVNNL-AETVTDEDLKKIFGHFGTITSAIVMKDSDGKSRCFGFVNFQSPDAAAA 262
PK + +++ NL + V+ EDL +IF +G I I +K++ FGF+ F +P +
Sbjct: 1 PK-SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQ-INIKNA------FGFIQFDNPQSVRD 52
Query: 263 AVE 265
A+E
Sbjct: 53 AIE 55
>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 = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 29 SLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANAKEA 88
S+YVG+++ L FS + + + D+ GYAY+ ++ +++ +A A
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVA 96
Query: 89 LNFMPINGKPIRIM 102
++ G+ I+++
Sbjct: 97 MDETVFRGRTIKVL 110
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 16/94 (17%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKM 175
+V++ N+D + L F++ G++ + D +G KGY +++F + A+ M
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 176 LNGMLINDKQVYVGLFVRRQERAQQNVSPKFTNV 209
D+ V+ G ++ V PK TN+
Sbjct: 98 -------DETVFRGRTIK--------VLPKRTNM 116
>pdb|1VBK|A Chain A, Crystal Structure Of Ph1313 From Pyrococcus Horikoshii Ot3
pdb|1VBK|B Chain B, Crystal Structure Of Ph1313 From Pyrococcus Horikoshii Ot3
Length = 307
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 10/72 (13%)
Query: 206 FTNVYVNNLAETVTDEDL--KKIFGHFGTITSAIVMKDSDGKS-----RCFGFVNFQSPD 258
F + +NN+ E + E++ K+IF G I IV +S ++ R FG V+
Sbjct: 22 FEKILMNNIREALVTEEVPYKEIFSRHGRI---IVKTNSPKEAANVLVRVFGIVSISPAM 78
Query: 259 AAAAAVEKLNGT 270
A++EK+N T
Sbjct: 79 EVEASLEKINRT 90
>pdb|3QXY|A Chain A, Human Setd6 In Complex With Rela Lys310
pdb|3QXY|B Chain B, Human Setd6 In Complex With Rela Lys310
pdb|3RC0|A Chain A, Human Setd6 In Complex With Rela Lys310 Peptide
pdb|3RC0|B Chain B, Human Setd6 In Complex With Rela Lys310 Peptide
Length = 449
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 140 GTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYVGLFVRRQERAQ 199
G LS KVA+ G GYG V E+ +A + + L++ +G + R+ A
Sbjct: 33 GLELSPKVAVSRQGTVAGYGMVARESVQAGELLFVVPRAALLSQHTCSIGGLLERERVAL 92
Query: 200 QNVS 203
Q+ S
Sbjct: 93 QSQS 96
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 144 SCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLNGMLINDKQVYV 188
+ V +D+NGQ G VQF+NE+ A+ + + L+ +N ++ +V
Sbjct: 45 AVHVLVDNNGQGLGQALVQFKNEDDARKS-ERLHRKKLNGREAFV 88
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.0 bits (66), Expect = 3.7, Method: Composition-based stats.
Identities = 20/88 (22%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 312 LYLKNLDDSINDEKLKELFSEFGTITSCKV----MVD-----QHGFSKGSGFAAFSMPEE 362
++++ L +++ E + + F + G I + K M++ + G KG +F P
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 363 ATRALNEMNGKMIGRKPLYVAVAQRKEE 390
A A++ +GK P+ V+ A R+ +
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRRAD 97
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.0 bits (66), Expect = 4.0, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 116 GNVFIKNLDTSIDNKALCDTFAAFG-TVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAI 173
++++ +L+ +D + FA G TV+S K+ + G GY FV+F + A+ +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 174 KMLNG 178
+NG
Sbjct: 70 HKING 74
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 8/79 (10%)
Query: 26 GNVSLYVGDLEQNVNESQLYDLFSQVAQVVSVRVCRDQSKRSSLGYAYVNYSNPQDAANA 85
+ L+VG++ +L F + V+ + +D YA+V+ +DA A
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEA 60
Query: 86 KEALNFMPINGKPIRIMYS 104
L+ GK + + S
Sbjct: 61 IRGLDNTEFQGKRMHVQLS 79
>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 = 29.6 bits (65), Expect = 4.8, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 116 GNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIK 174
G I + + KAL F+ G V++ + ID + G++KG+ FV+ + A+ IK
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
Query: 175 MLNGMLINDKQ 185
+G ++ K
Sbjct: 73 SFHGKRLDLKH 83
>pdb|2ZQV|A Chain A, Crystal Structure Of A Mutant Pin1 Peptidyl-Prolyl
Cis-Trans Isomerase
Length = 163
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 71 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 128
Query: 352 SGFAAFSMPEEATRALN--EMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 129 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 160
>pdb|2ZR5|A Chain A, Crystal Structure Of A Mutant Pin1 Peptidyl-Prolyl
Cis-Trans Isomerase
Length = 163
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 71 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 128
Query: 352 SGFAAFSMPEEATRAL--NEMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 129 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 160
>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 = 29.6 bits (65), Expect = 5.5, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 116 GNVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAID-SNGQSKGYGFVQFENEEAAQNAIK 174
G I + + KAL F+ G V++ + ID + G++KG+ FV+ + A+ IK
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
Query: 175 MLNGMLINDKQ 185
+G ++ K
Sbjct: 73 SFHGKRLDLKH 83
>pdb|2ITK|A Chain A, Human Pin1 Bound To D-Peptide
pdb|2Q5A|A Chain A, Human Pin1 Bound To L-Peptide
pdb|3KAB|A Chain A, Structure-Guided Design Of Alpha-Amino Acid-Derived Pin1
Inhibitors
pdb|3KAG|A Chain A, Structure-Guided Design Of Alpha-Amino Acid-Derived Pin1
Inhibitors
pdb|3KAH|A Chain A, Structure-Guided Design Of Alpha-Amino Acid-Derived Pin1
Inhibitors
pdb|3KAI|A Chain A, Structure-Guided Design Of Alpha-Amino Acid-Derived Pin1
Inhibitors
pdb|3KCE|A Chain A, Structure-Guided Design Of Alpha-Amino Acid-Derived Pin1
Inhibitors
pdb|3ODK|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|2XP3|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|2XP4|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|2XP5|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|2XP7|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|2XP8|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|2XP9|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|2XPA|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|2XPB|A Chain A, Discovery Of Cell-Active Phenyl-Imidazole Pin1 Inhibitors
By Structure-Guided Fragment Evolution
pdb|3NTP|A Chain A, Human Pin1 Complexed With Reduced Amide Inhibitor
Length = 167
Score = 29.6 bits (65), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 75 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 132
Query: 352 SGFAAFSMPEEATRAL--NEMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 133 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 164
>pdb|2F21|A Chain A, Human Pin1 Fip Mutant
Length = 162
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 70 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 127
Query: 352 SGFAAFSMPEEATRAL--NEMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 128 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 159
>pdb|2ZR6|A Chain A, Crystal Structure Of A Mutant Pin1 Peptidyl-Prolyl
Cis-Trans Isomerase
pdb|3OOB|A Chain A, Structural And Functional Insights Of Directly Targeting
Pin1 By Epigallocatechin-3-Gallate
Length = 163
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 71 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 128
Query: 352 SGFAAFSMPEEATRAL--NEMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 129 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 160
>pdb|1PIN|A Chain A, Pin1 Peptidyl-Prolyl Cis-Trans Isomerase From Homo Sapiens
pdb|1NMV|A Chain A, Solution Structure Of Human Pin1
Length = 163
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 71 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 128
Query: 352 SGFAAFSMPEEATRALN--EMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 129 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 160
>pdb|3TC5|A Chain A, Selective Targeting Of Disease-Relevant Protein Binding
Domains By O- Phosphorylated Natural Product Derivatives
Length = 166
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 74 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 131
Query: 352 SGFAAFSMPEEATRAL--NEMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 132 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 163
>pdb|1F8A|B Chain B, Structural Basis For The Phosphoserine-Proline Recognition
By Group Iv Ww Domains
Length = 167
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 75 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 132
Query: 352 SGFAAFSMPEEATRAL--NEMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 133 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 164
>pdb|2ZR4|A Chain A, Crystal Structure Of A Mutant Pin1 Peptidyl-Prolyl
Cis-Trans Isomerase
Length = 163
Score = 29.6 bits (65), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 71 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 128
Query: 352 SGFAAFSMPEEATRALN--EMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 129 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 160
>pdb|2ZQU|A Chain A, Crystal Structure Of A Mutant Pin1 Peptidyl-Prolyl
Cis-Trans Isomerase
Length = 163
Score = 29.6 bits (65), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 71 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 128
Query: 352 SGFAAFSMPEEATRALN--EMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 129 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 160
>pdb|1ZCN|A Chain A, Human Pin1 Ng Mutant
Length = 161
Score = 29.3 bits (64), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 69 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDCSSAKARGDLGAFSRG 126
Query: 352 SGFAAFSMPEEATRAL--NEMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 127 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 158
>pdb|2ZQT|A Chain A, Crystal Structure Of A Mutant Pin1 Peptidyl-Prolyl
Cis-Trans Isomerase
Length = 163
Score = 29.3 bits (64), Expect = 6.8, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 71 SSWRQEKITRTKEEALELINGYIQKIKSG--EEDFESLASQFSDCSSAKARGDLGAFSRG 128
Query: 352 SGFAAFSMPEEATRAL--NEMNG 372
F E+A+ AL EM+G
Sbjct: 129 QAQKPF---EDASFALRTGEMSG 148
>pdb|2ZQS|A Chain A, Crystal Structure Of A Mutant Pin1 Peptidyl-Prolyl
Cis-Trans Isomerase
Length = 163
Score = 29.3 bits (64), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 9/95 (9%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 71 SSWRQEKITRTKEEALELINGYIQKIKS--GEEDFESLASQFSDASSAKARGDLGAFSRG 128
Query: 352 SGFAAFSMPEEATRALN--EMNGKMIGRKPLYVAV 384
F E+A+ AL EM+G + +++ +
Sbjct: 129 QMQKPF---EDASFALRTGEMSGPVFTDSGIHIIL 160
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 29.3 bits (64), Expect = 7.3, Method: Composition-based stats.
Identities = 30/153 (19%), Positives = 61/153 (39%), Gaps = 16/153 (10%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDSNGQSKGYGFVQFENEEAAQNAIKMLN 177
V +KNL S + + F G ++ VA DS ++ + ++F + A AI +
Sbjct: 7 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTH 65
Query: 178 GMLINDKQVYVGLFVRRQERAQQNVSPKFTNVYVNNLAETVTDEDLKKIFGHFGTITSAI 237
++ ++ V +++ N + T +++ + + +I
Sbjct: 66 -KVVGQNEIIVSHLTE-------------CTLWMTNFPPSYTQRNIRDLLQDINVVALSI 111
Query: 238 VMKDSD-GKSRCFGFVNFQSPDAAAAAVEKLNG 269
+ SR F +++ S + A VEKLNG
Sbjct: 112 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG 144
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 28.9 bits (63), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 147 VAIDSNGQSKGYGFVQFENEEAAQNAIK 174
+ +D G+S G FVQF ++E A+ A+K
Sbjct: 48 LPVDFQGRSTGEAFVQFASQEIAEKALK 75
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 28.9 bits (63), Expect = 8.6, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 118 VFIKNLDTSIDNKALCDTFAAFGTVL---SCKVAIDSNGQSKGYGFVQFENEEAAQNAIK 174
VF+ L ID + +F FG ++ K S KGY F+ F+ E + Q
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQ---A 67
Query: 175 MLNGMLINDKQVYV 188
+++ L D ++Y+
Sbjct: 68 LIDACLEEDGKLYL 81
>pdb|1NMW|A Chain A, Solution Structure Of The Ppiase Domain Of Human Pin1
Length = 114
Score = 28.9 bits (63), Expect = 9.2, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 294 AKFEQERISRY--EKLKGANLYLKNLDDSINDEKLKELFSEFGTITSCKVMVDQHGFSKG 351
+ + QE+I+R E L+ N Y++ + +E + L S+F +S K D FS+G
Sbjct: 22 SSWRQEKITRTKEEALELINGYIQKIKSG--EEDFESLASQFSDCSSAKARGDLGAFSRG 79
Query: 352 SGFAAFSMPEEATRAL--NEMNG 372
F E+A+ AL EM+G
Sbjct: 80 QMQKPF---EDASFALRTGEMSG 99
>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 = 28.9 bits (63), Expect = 9.9, Method: Composition-based stats.
Identities = 16/73 (21%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 117 NVFIKNLDTSIDNKALCDTFAAFGTVLSCKVAIDS-NGQSKGYGFVQFENEEAAQNAIKM 175
++++ N+D + L F G+V + D +G KG+ +++F ++E+ + ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 65
Query: 176 LNGMLINDKQVYV 188
L+ L +Q+ V
Sbjct: 66 LDESLFRGRQIKV 78
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 0.133 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,518,391
Number of Sequences: 62578
Number of extensions: 725910
Number of successful extensions: 2518
Number of sequences better than 100.0: 237
Number of HSP's better than 100.0 without gapping: 164
Number of HSP's successfully gapped in prelim test: 73
Number of HSP's that attempted gapping in prelim test: 1666
Number of HSP's gapped (non-prelim): 691
length of query: 637
length of database: 14,973,337
effective HSP length: 105
effective length of query: 532
effective length of database: 8,402,647
effective search space: 4470208204
effective search space used: 4470208204
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: 55 (25.8 bits)