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= 002168
(957 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 70.5 bits (171), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 47/153 (30%), Positives = 79/153 (51%), Gaps = 17/153 (11%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAKAAK 73
+NL V L + T + K LFG G + DK+T S + FV + DA A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITG-QSLGYGFVNYSDPNDADKAI 63
Query: 74 DALQGSDFRGNPIKIEFARPAKPS---KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFL 130
+ L G + IK+ +ARP+ S +L+V G+ +T+S++E+E+ F ++G I + L
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRIL 123
Query: 131 KDGNT------AFVEYSRLEDAAEALKNINGRQ 157
D T F+ + + +A EA+K +NG++
Sbjct: 124 LDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 156
Score = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 47/97 (48%), Gaps = 15/97 (15%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALKN 152
+L V + Q ++++E + F G+IE K ++D T FV YS DA +A+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 153 INGRQIGGEQLRVDFLRSQPSRREQWPNSHDARDGPI 189
+NG ++ + ++V + R P+S RD +
Sbjct: 66 LNGLKLQTKTIKVSYAR---------PSSASIRDANL 93
>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 = 69.7 bits (169), Expect = 7e-12, Method: Composition-based stats.
Identities = 50/165 (30%), Positives = 86/165 (52%), Gaps = 19/165 (11%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAKAAK 73
+NL V L + T + + LFG G + DK+T S + FV + +DA+ A
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITG-QSLGYGFVNYIDPKDAEKAI 61
Query: 74 DALQGSDFRGNPIKIEFARPAKPS---KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFL 130
+ L G + IK+ +ARP+ S +L+V G+ +T++++ELE+ F ++G I + L
Sbjct: 62 NTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRIL 121
Query: 131 KDGNT------AFVEYSRLEDAAEALKNINGRQIGG--EQLRVDF 167
D T F+ + + +A EA+K +NG++ G E + V F
Sbjct: 122 VDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF 166
Score = 36.6 bits (83), Expect = 0.078, Method: Composition-based stats.
Identities = 26/95 (27%), Positives = 44/95 (46%), Gaps = 15/95 (15%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALKN 152
+L V + Q +++EE F G IE K ++D T FV Y +DA +A+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 153 INGRQIGGEQLRVDFLRSQPSRREQWPNSHDARDG 187
+NG ++ + ++V + R P+S RD
Sbjct: 64 LNGLRLQTKTIKVSYAR---------PSSASIRDA 89
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 67.4 bits (163), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 43/153 (28%), Positives = 80/153 (52%), Gaps = 17/153 (11%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAKAAK 73
+NL V L + T +L+ LF G + DKV +S + FV + +DA+ A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHS-LGYGFVNYVTAKDAERAI 61
Query: 74 DALQGSDFRGNPIKIEFARPAK---PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFL 130
+ L G + IK+ +ARP+ +L++ G+ +T++++++E+ F +FG I + + L
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 131 KDGNT------AFVEYSRLEDAAEALKNINGRQ 157
D T AF+ + + +A EA+ + NG +
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
Score = 37.0 bits (84), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKD---GNT---AFVEYSRLEDAAEALKN 152
+L V + Q ++++EL F G +E K ++D G++ FV Y +DA A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 153 INGRQIGGEQLRVDFLR 169
+NG ++ + ++V + R
Sbjct: 64 LNGLRLQSKTIKVSYAR 80
Score = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 43/93 (46%), Gaps = 8/93 (8%)
Query: 7 KFNRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFG------ALDKVTTYSSRSFAF 60
K + A E +NL++ L T D++++F +FG L TT SR AF
Sbjct: 75 KVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAF 134
Query: 61 VYFKRVEDAKAAKDALQGSDFRGN--PIKIEFA 91
+ F + +A+ A + G G+ PI + FA
Sbjct: 135 IRFDKRSEAEEAITSFNGHKPPGSSEPITVXFA 167
>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 = 67.0 bits (162), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 43/153 (28%), Positives = 80/153 (52%), Gaps = 17/153 (11%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAKAAK 73
+NL V L + T +L+ LF G + DKV +S + FV + +DA+ A
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHS-LGYGFVNYVTAKDAERAI 61
Query: 74 DALQGSDFRGNPIKIEFARPAK---PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFL 130
+ L G + IK+ +ARP+ +L++ G+ +T++++++E+ F +FG I + + L
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 131 KDGNT------AFVEYSRLEDAAEALKNINGRQ 157
D T AF+ + + +A EA+ + NG +
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
Score = 37.0 bits (84), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKD---GNT---AFVEYSRLEDAAEALKN 152
+L V + Q ++++EL F G +E K ++D G++ FV Y +DA A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 153 INGRQIGGEQLRVDFLR 169
+NG ++ + ++V + R
Sbjct: 64 LNGLRLQSKTIKVSYAR 80
Score = 36.6 bits (83), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKELFGKFG------ALDKVTTYSSRSFAFVYFKRVEDA 69
E +NL++ L T D++++F +FG L TT SR AF+ F + +A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 70 KAAKDALQGSDFRGN--PIKIEFA 91
+ A + G G+ PI ++FA
Sbjct: 144 EEAITSFNGHKPPGSSEPITVKFA 167
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 64.7 bits (156), Expect = 2e-10, Method: Composition-based stats.
Identities = 47/150 (31%), Positives = 75/150 (50%), Gaps = 15/150 (10%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAAK 73
++NL V L D TD +L LF G ++ T S +AFV F D++ A
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 74 DALQGSDFRGNPIKIEFARPAKPS---KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFL 130
L G R +K+ +ARP S +L+V + +T++ ++L+ F K+G+I L
Sbjct: 63 KVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Query: 131 KDGNT------AFVEYSRLEDAAEALKNIN 154
+D T AFV Y++ E+A EA+ +N
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 38.9 bits (89), Expect = 0.013, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 7 KFNRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFA 59
K + A E+ +NL+V NL TD L +FGK+G++ DK+T R A
Sbjct: 76 KVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG-RPRGVA 134
Query: 60 FVYFKRVEDAKAAKDAL 76
FV + + E+A+ A AL
Sbjct: 135 FVRYNKREEAQEAISAL 151
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKN 152
+L V + Q ++ EL F G I + ++D T AFV+++ D+ A+K
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 153 INGRQIGGEQLRVDFLR 169
+NG + ++L+V + R
Sbjct: 65 LNGITVRNKRLKVSYAR 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 = 63.9 bits (154), Expect = 4e-10, Method: Composition-based stats.
Identities = 49/151 (32%), Positives = 76/151 (50%), Gaps = 17/151 (11%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAKAA 72
++NL V L D TD +L LF G + D T YS +AFV F D++ A
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSF-GYAFVDFTSEXDSQRA 72
Query: 73 KDALQGSDFRGNPIKIEFARPAKPS---KHLWVGGISQTVSKEELEEGFLKFGNIEDFKF 129
L G R +K+ +ARP S +L+V + +T++ ++L+ F K+G+I
Sbjct: 73 IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 130 LKDGNT------AFVEYSRLEDAAEALKNIN 154
L+D T AFV Y++ E+A EA+ +N
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 38.5 bits (88), Expect = 0.020, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 7 KFNRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFA 59
K + A E+ +NL+V NL TD L +FGK+G++ DK+T R A
Sbjct: 87 KVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG-RPRGVA 145
Query: 60 FVYFKRVEDAKAAKDAL 76
FV + + E+A+ A AL
Sbjct: 146 FVRYNKREEAQEAISAL 162
Score = 32.3 bits (72), Expect = 1.4, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 93 PAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDA 146
P + +L V + Q + EL F G I + +D T AFV+++ D+
Sbjct: 10 PRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDS 69
Query: 147 AEALKNINGRQIGGEQLRVDFLR 169
A+K +NG + ++L+V + R
Sbjct: 70 QRAIKVLNGITVRNKRLKVSYAR 92
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 63.2 bits (152), Expect = 6e-10, Method: Composition-based stats.
Identities = 44/134 (32%), Positives = 65/134 (48%), Gaps = 8/134 (5%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQGSDFR 82
L+VGNL D T+ D K LF ++G +V R F F+ + A+ AK L G+ +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84
Query: 83 GNPIKIEFARPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDG-----NTAF 137
P++I FA L V +S VS E LE+ F +FG +E + D F
Sbjct: 85 SRPLRIRFATHGAA---LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGF 141
Query: 138 VEYSRLEDAAEALK 151
VE++ A +AL+
Sbjct: 142 VEFAAKPPARKALE 155
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 63.2 bits (152), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 37/94 (39%), Positives = 54/94 (57%), Gaps = 10/94 (10%)
Query: 9 NRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVY 62
NRA D P+ L V LS TT+ DL+E+F K+G + V+ + SR FAFVY
Sbjct: 39 NRANPD----PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94
Query: 63 FKRVEDAKAAKDALQGSDFRGNPIKIEFARPAKP 96
F+ V+DAK AK+ G + G I+++F+ +P
Sbjct: 95 FENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 96 PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEA 149
P+ L V G+S ++ +L E F K+G I D + D + AFV + ++DA EA
Sbjct: 45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 150 LKNINGRQIGGEQLRVDF 167
+ NG ++ G ++RVDF
Sbjct: 105 KERANGMELDGRRIRVDF 122
Score = 34.7 bits (78), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 8/89 (8%)
Query: 215 NRDGP-PSKILWVGYPPSVQMDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRS 267
NR P P+ L V + S+ E+ L +G I + +S SR ++FV F +
Sbjct: 39 NRANPDPNCCLGV-FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97
Query: 268 VDEARRAKEGLQGRLFNDPRITIMFSSSE 296
VD+A+ AKE G + RI + FS ++
Sbjct: 98 VDDAKEAKERANGMELDGRRIRVDFSITK 126
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 61.6 bits (148), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/84 (39%), Positives = 50/84 (59%), Gaps = 6/84 (7%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAA 72
P+ L V LS TT+ DL+E+F K+G + V+ + SR FAFVYF+ V+DAK A
Sbjct: 14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 73 KDALQGSDFRGNPIKIEFARPAKP 96
K+ G + G I+++F+ +P
Sbjct: 74 KERANGMELDGRRIRVDFSITKRP 97
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 96 PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEA 149
P+ L V G+S ++ +L E F K+G I D + D + AFV + ++DA EA
Sbjct: 14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 150 LKNINGRQIGGEQLRVDF 167
+ NG ++ G ++RVDF
Sbjct: 74 KERANGMELDGRRIRVDF 91
Score = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 215 NRDGPPSKILWVGYPPSVQMDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSV 268
NR P + S+ E+ L +G I + +S SR ++FV F +V
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 269 DEARRAKEGLQGRLFNDPRITIMFS 293
D+A+ AKE G + RI + FS
Sbjct: 68 DDAKEAKERANGMELDGRRIRVDFS 92
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 61.6 bits (148), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/84 (39%), Positives = 50/84 (59%), Gaps = 6/84 (7%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAA 72
P+ L V LS TT+ DL+E+F K+G + V+ + SR FAFVYF+ V+DAK A
Sbjct: 11 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
Query: 73 KDALQGSDFRGNPIKIEFARPAKP 96
K+ G + G I+++F+ +P
Sbjct: 71 KERANGMELDGRRIRVDFSITKRP 94
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 96 PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEA 149
P+ L V G+S ++ +L E F K+G I D + D + AFV + ++DA EA
Sbjct: 11 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
Query: 150 LKNINGRQIGGEQLRVDF 167
+ NG ++ G ++RVDF
Sbjct: 71 KERANGMELDGRRIRVDF 88
Score = 32.7 bits (73), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 220 PSKILWVGYPPSVQMDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARR 273
P+ L V + S+ E+ L +G I + +S SR ++FV F +VD+A+
Sbjct: 11 PNCCLGV-FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 69
Query: 274 AKEGLQGRLFNDPRITIMFSSSE 296
AKE G + RI + FS ++
Sbjct: 70 AKERANGMELDGRRIRVDFSITK 92
>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 = 61.2 bits (147), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 45/175 (25%), Positives = 86/175 (49%), Gaps = 17/175 (9%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAA 72
P ++L+VG+L D T+A L E F G + + T S +A+V F++ DA+ A
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
Query: 73 KDALQGSDFRGNPIKIEFARPAKPS------KHLWVGGISQTVSKEELEEGFLKFGNIED 126
D + +G P++I +++ PS ++++ + +++ + L + F FGNI
Sbjct: 74 LDTMNFDVIKGKPVRIMWSQ-RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 132
Query: 127 FKFLKDGNTA----FVEYSRLEDAAEALKNINGRQIGGEQLRVDFLRSQPSRREQ 177
K + D N + FV + E A A++ +NG + ++ V +S+ R +
Sbjct: 133 CKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 187
Score = 46.6 bits (109), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 49/208 (23%), Positives = 77/208 (37%), Gaps = 53/208 (25%)
Query: 93 PAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDA 146
P+ P L+VG + V++ L E F G I + +D T A+V + + DA
Sbjct: 11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70
Query: 147 AEALKNINGRQIGGEQLRVDFLRSQPSRREQWPNSHDARDGPIIGRGTGFSDNHSAYKRS 206
AL +N I G+ +R+ + + PS R+ G G F N
Sbjct: 71 ERALDTMNFDVIKGKPVRIMWSQRDPSLRKS-------------GVGNIFIKNLDK---- 113
Query: 207 HPQSSVGRNRDGPPSKILWVGYPPSVQMDEQMLHNAMILFGEIERIKSYP----SRNYSF 262
+D + L++ FG I K S+ Y F
Sbjct: 114 --------------------------SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF 147
Query: 263 VEFRSVDEARRAKEGLQGRLFNDPRITI 290
V F + + A RA E + G L ND ++ +
Sbjct: 148 VHFETQEAAERAIEKMNGMLLNDRKVFV 175
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 60.5 bits (145), Expect = 5e-09, Method: Composition-based stats.
Identities = 46/146 (31%), Positives = 68/146 (46%), Gaps = 8/146 (5%)
Query: 10 RAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDA 69
R +K S L+VGNL D T+ ++++LF K+G +V + + F F+ + A
Sbjct: 12 RKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLA 71
Query: 70 KAAKDALQGSDFRGNPIKIEFARPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKF 129
+ AK L RG +++ F A S L V + Q VS E LEE F FG +E
Sbjct: 72 EIAKVELDNMPLRGKQLRVRF---ACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVV 128
Query: 130 LKD-----GNTAFVEYSRLEDAAEAL 150
+ D VE+S A +AL
Sbjct: 129 IVDDRGRPSGKGIVEFSGKPAARKAL 154
Score = 31.2 bits (69), Expect = 3.0, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 90 FARPAKPS----KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLED 145
F +P + + L+VG + +++EE+ + F K+G + KD F+
Sbjct: 11 FRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTL 70
Query: 146 AAEALKNINGRQIGGEQLRVDF 167
A A ++ + G+QLRV F
Sbjct: 71 AEIAKVELDNMPLRGKQLRVRF 92
>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 = 60.5 bits (145), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 79/163 (48%), Gaps = 21/163 (12%)
Query: 23 LWVGNLSADTTDADLKELFG---KFGALDK--------VTTYSSRSFAFVYFKRVEDAKA 71
L+VGN+ T+ + + F + G L + V ++FAF+ F+ V++
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 72 AKDALQGSDFRGNPIKIEFARPAKP---SKHLWVGGISQTVSKEELEEGFLKFGNIEDFK 128
A A G F+G +KI +P + L++GG+ ++ ++++E FG ++ F
Sbjct: 69 AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 127
Query: 129 FLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRV 165
+KD T AF EY + +A+ +NG Q+G ++L V
Sbjct: 128 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
Score = 30.8 bits (68), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 224 LWVGYPPSVQMDEQML--HNAMILFGEIERIKSYP--------SRNYSFVEFRSVDEARR 273
L+VG P +E M+ NA + G + + P +N++F+EFRSVDE +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 274 A 274
A
Sbjct: 69 A 69
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 60.1 bits (144), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 79/163 (48%), Gaps = 21/163 (12%)
Query: 23 LWVGNLSADTTDADLKELFG---KFGALDK--------VTTYSSRSFAFVYFKRVEDAKA 71
L+VGN+ T+ + + F + G L + V ++FAF+ F+ V++
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 72 AKDALQGSDFRGNPIKIEFARPAKP---SKHLWVGGISQTVSKEELEEGFLKFGNIEDFK 128
A A G F+G +KI +P + L++GG+ ++ ++++E FG ++ F
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 125
Query: 129 FLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRV 165
+KD T AF EY + +A+ +NG Q+G ++L V
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
Score = 30.8 bits (68), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 224 LWVGYPPSVQMDEQML--HNAMILFGEIERIKSYP--------SRNYSFVEFRSVDEARR 273
L+VG P +E M+ NA + G + + P +N++F+EFRSVDE +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 274 A 274
A
Sbjct: 67 A 67
>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 = 59.7 bits (143), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 45/175 (25%), Positives = 86/175 (49%), Gaps = 17/175 (9%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAA 72
P ++L+VG+L D T+A L E F G + + T S +A+V F++ DA+ A
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
Query: 73 KDALQGSDFRGNPIKIEFARPAKPS------KHLWVGGISQTVSKEELEEGFLKFGNIED 126
D + +G P++I +++ PS ++++ + +++ + L + F FGNI
Sbjct: 69 LDTMNFDVIKGKPVRIMWSQ-RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 127
Query: 127 FKFLKDGNTA----FVEYSRLEDAAEALKNINGRQIGGEQLRVDFLRSQPSRREQ 177
K + D N + FV + E A A++ +NG + ++ V +S+ R +
Sbjct: 128 CKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 19/92 (20%)
Query: 218 GPPSKILWVGYPPSVQ---------------MDEQMLHNAMILFGEIERIKSYPSRN--- 259
G P +I+W PS++ +D + L++ FG I K N
Sbjct: 79 GKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK 138
Query: 260 -YSFVEFRSVDEARRAKEGLQGRLFNDPRITI 290
Y FV F + + A RA E + G L ND ++ +
Sbjct: 139 GYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
>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 = 57.4 bits (137), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 38/171 (22%), Positives = 78/171 (45%), Gaps = 26/171 (15%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAAKD 74
S ++VG++ + + +++ F FG + + T + FAFV ++ E A+ A +
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 75 ALQGSDFRGNPIKI--------------EFARPAKPSKHLWVGGISQTVSKEELEEGFLK 120
+ G IK+ + A A+ ++V + Q +S ++++ F
Sbjct: 89 QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 148
Query: 121 FGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRV 165
FG I+ +D T F+EY + + + +A+ ++N +GG+ LRV
Sbjct: 149 FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
Score = 33.1 bits (74), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 16/80 (20%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 15 KEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVED 68
+EA + ++V ++ D +D D+K +F FG + TT + + F+ +++ +
Sbjct: 120 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS 179
Query: 69 AKAAKDALQGSDFRGNPIKI 88
++ A ++ D G +++
Sbjct: 180 SQDAVSSMNLFDLGGQYLRV 199
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 57.0 bits (136), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 48/89 (53%), Gaps = 3/89 (3%)
Query: 87 KIEFARPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDA 146
KI + + A P+ LWVGG+ S L F +FG+I +K + A+++Y L+ A
Sbjct: 8 KIGYGK-ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAA 66
Query: 147 AEALKNINGRQIGG--EQLRVDFLRSQPS 173
A + G +GG +LRVDF +S PS
Sbjct: 67 QAACAKMRGFPLGGPDRRLRVDFAKSGPS 95
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
+A P++ LWVG L +T+ A L F +FG++ + SFA++ ++ ++ A+AA
Sbjct: 13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK 72
Query: 76 LQGSDFRG--NPIKIEFAR 92
++G G ++++FA+
Sbjct: 73 MRGFPLGGPDRRLRVDFAK 91
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 57.0 bits (136), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 34/78 (43%), Positives = 46/78 (58%), Gaps = 3/78 (3%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKFGALDKVT---TYSSRSFAFVYFKRVEDAKAAKDA 75
PS L+V LS DTT+ LKE F VT T SS+ F FV F EDAKAAK+A
Sbjct: 14 PSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 76 LQGSDFRGNPIKIEFARP 93
++ + GN + +++A+P
Sbjct: 74 MEDGEIDGNKVTLDWAKP 91
Score = 33.5 bits (75), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 3/79 (3%)
Query: 94 AKPSKHLWVGGISQTVSKEELEEGF---LKFGNIEDFKFLKDGNTAFVEYSRLEDAAEAL 150
++PSK L+V G+S+ ++E L+E F ++ + D + FV+++ EDA A
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 151 KNINGRQIGGEQLRVDFLR 169
+ + +I G ++ +D+ +
Sbjct: 72 EAMEDGEIDGNKVTLDWAK 90
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 56.6 bits (135), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 45/76 (59%), Gaps = 6/76 (7%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAA 72
P+ L V LS TT+ DL+E+F K+G + V+ + SR FAFVYF+ V+DAK A
Sbjct: 14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 73 KDALQGSDFRGNPIKI 88
K+ G + G I++
Sbjct: 74 KERANGMELDGRRIRV 89
Score = 43.1 bits (100), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 96 PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEA 149
P+ L V G+S ++ +L E F K+G I D + D + AFV + ++DA EA
Sbjct: 14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 150 LKNINGRQIGGEQLRV 165
+ NG ++ G ++RV
Sbjct: 74 KERANGMELDGRRIRV 89
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 8/83 (9%)
Query: 215 NRDGP-PSKILWVGYPPSVQMDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRS 267
NR P P+ L V + S+ E+ L +G I + +S SR ++FV F +
Sbjct: 8 NRANPDPNCCLGV-FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 268 VDEARRAKEGLQGRLFNDPRITI 290
VD+A+ AKE G + RI +
Sbjct: 67 VDDAKEAKERANGMELDGRRIRV 89
>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 = 56.2 bits (134), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 37/171 (21%), Positives = 77/171 (45%), Gaps = 26/171 (15%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAAKD 74
++VG++ + + +++ F FG + + T + FAFV ++ E A+ A +
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 75 ALQGSDFRGNPIKI--------------EFARPAKPSKHLWVGGISQTVSKEELEEGFLK 120
+ G IK+ + A A+ ++V + Q +S ++++ F
Sbjct: 74 QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 133
Query: 121 FGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRV 165
FG I+ +D T F+EY + + + +A+ ++N +GG+ LRV
Sbjct: 134 FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
Score = 32.7 bits (73), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 16/80 (20%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 15 KEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVED 68
+EA + ++V ++ D +D D+K +F FG + TT + + F+ +++ +
Sbjct: 105 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 164
Query: 69 AKAAKDALQGSDFRGNPIKI 88
++ A ++ D G +++
Sbjct: 165 SQDAVSSMNLFDLGGQYLRV 184
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 33/101 (32%), Positives = 51/101 (50%), Gaps = 16/101 (15%)
Query: 94 AKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAA 147
A L+VGG+S +++ LE+ F K+G I + +KD T FV + ++DA
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 148 EALKNINGRQIGGEQLRVDFLRSQPSRREQWPNSHDARDGP 188
+A+ +NG+ + G Q+RVD Q S D R GP
Sbjct: 69 DAMMAMNGKSVDGRQIRVD----------QAGKSSDNRSGP 99
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 17 APPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAK 70
A L+VG LS DT + L+++F K+G + +V T SR F FV F+ ++DAK
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 71 AAKDALQGSDFRGNPIKIEFA 91
A A+ G G I+++ A
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQA 89
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 51/90 (56%), Gaps = 6/90 (6%)
Query: 14 DKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVE 67
++ A ++ + V NLS DT + DL+ELF FG++ ++ TT S+ FAF+ F R E
Sbjct: 9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 68 DAKAAKDALQGSDFRGNPIKIEFARPAKPS 97
DA A + G + + +E+A+P+ S
Sbjct: 69 DAARAIAGVSGFGYDHLILNVEWAKPSTNS 98
Score = 37.7 bits (86), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 92 RPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLED 145
R A + + V +S+ + +L+E F FG+I KD T AF+ + R ED
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 146 AAEALKNINGRQIGGEQLRVDFLRSQPS 173
AA A+ ++G G + L ++ ++PS
Sbjct: 70 AARAIAGVSG--FGYDHLILNVEWAKPS 95
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 42/161 (26%), Positives = 73/161 (45%), Gaps = 16/161 (9%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS-----FAFVYFKRVEDAKAAKDALQ 77
L+VGNL T+ LK+ F G + + ++ +AFV + + DA A L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 78 GSDFRGNPIKIEFARPAKPSK-----HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKD 132
G N +KI +A ++ S +L+VG ++ V E L F F + + D
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 122
Query: 133 GNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRVDF 167
T FV ++ +DA A+ ++ G+ + G LR+++
Sbjct: 123 MQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 163
Score = 51.2 bits (121), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 49/93 (52%), Gaps = 8/93 (8%)
Query: 7 KFNRAYDDKEAPPSS--NLWVGNLSADTTDADLKELFGKF------GALDKVTTYSSRSF 58
K N A+ +++ NL+VG+L+ + D L+ F F + + T SSR +
Sbjct: 72 KINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGY 131
Query: 59 AFVYFKRVEDAKAAKDALQGSDFRGNPIKIEFA 91
FV F +DA+ A D++QG D G P++I +A
Sbjct: 132 GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 49.7 bits (117), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 50/197 (25%), Positives = 86/197 (43%), Gaps = 56/197 (28%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT-----AFVEYSRLEDAAEALKNIN 154
L+VG + + ++++ L++ F G I + K + D N AFVEY + DA AL+ +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 155 GRQIGGEQLRVDF-LRSQPSRREQWPNSHDARDGPIIGRGTGFSDNHSAYKRSHPQSSVG 213
G+QI +++++ +SQ S + N
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDTFN--------------------------------- 89
Query: 214 RNRDGPPSKILWVGYPPSVQMDEQMLHNAM-----ILFGEIER-IKSYPSRNYSFVEFRS 267
L+VG +V +D++ L NA L G + +++ SR Y FV F S
Sbjct: 90 ----------LFVG-DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138
Query: 268 VDEARRAKEGLQGRLFN 284
D+A+ A + +QG+ N
Sbjct: 139 QDDAQNAMDSMQGQDLN 155
>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 = 54.3 bits (129), Expect = 4e-07, Method: Composition-based stats.
Identities = 45/169 (26%), Positives = 83/169 (49%), Gaps = 22/169 (13%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKR---VEDAK 70
S +++G L+ DTT+ +L+E FGK+G + + T SR F F+ F++ V++
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 71 AAKDALQGSDFRGNPIKIEFARPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFL 130
+ L G +P + + ++VGGI V +E EE F ++G I D + +
Sbjct: 63 KTQHILDGKVI--DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120
Query: 131 KDGNT------AFVEYSRLEDAAEALKNI-NGRQIGGEQLRVDFLRSQP 172
D +T FV Y D+A+A+ + + I + +++ R++P
Sbjct: 121 LDKDTGQSRGFGFVTY----DSADAVDRVCQNKFIDFKDRKIEIKRAEP 165
Score = 32.7 bits (73), Expect = 1.1, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 95 KPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAE 148
K S +++GG++ +++ L E F K+G + D K +KD T F+ + + E
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 149 ALK 151
+K
Sbjct: 61 VVK 63
Score = 31.6 bits (70), Expect = 1.9, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 13/93 (13%)
Query: 10 RAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGA-------LDKVTTYSSRSFAFVY 62
RA E + ++VG + D + +E F ++G LDK T SR F FV
Sbjct: 77 RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-DTGQSRGFGFVT 135
Query: 63 FKRVEDAKAAKDALQGS--DFRGNPIKIEFARP 93
+ + A A Q DF+ I+I+ A P
Sbjct: 136 Y---DSADAVDRVCQNKFIDFKDRKIEIKRAEP 165
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 53.9 bits (128), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/94 (31%), Positives = 53/94 (56%), Gaps = 2/94 (2%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNINGRQ 157
K L+V ++ TV++E LE+ F +FG +E K LKD AF+ + + A +A++ +NG+
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--YAFIHFDERDGAVKAMEEMNGKD 69
Query: 158 IGGEQLRVDFLRSQPSRREQWPNSHDARDGPIIG 191
+ GE + + F + +R++ A GP G
Sbjct: 70 LEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQGSDFR 82
L+V NL+ T+ L++ F +FG L++V + +AF++F + A A + + G D
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLE 71
Query: 83 GNPIKIEFARP 93
G I+I FA+P
Sbjct: 72 GENIEIVFAKP 82
Score = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 3/94 (3%)
Query: 222 KILWVGYPPSVQMDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR 281
K+L+V + + E++L A FG++ER+K ++Y+F+ F D A +A E + G+
Sbjct: 12 KVLFVRNLANT-VTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGK 68
Query: 282 LFNDPRITIMFSSSELAPGKDYPGSYSGTKGPRS 315
I I+F+ K+ GP S
Sbjct: 69 DLEGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102
>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 = 53.5 bits (127), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 45/183 (24%), Positives = 80/183 (43%), Gaps = 41/183 (22%)
Query: 23 LWVGNLSADTTDADLKELFG---KFGALDK--------VTTYSSRSFAFVYFKRVEDAKA 71
L+VGN+ T+ + + F + G L + V ++FAF+ F+ V++
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 72 AKDALQGSDFRGNPIKIEFARPAKP----------------------SKH-LWVGGISQT 108
A A G F+G +KI +P S H L++GG+
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125
Query: 109 VSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQ 162
++ ++++E FG ++ F +KD T AF EY + +A+ +NG Q+G ++
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185
Query: 163 LRV 165
L V
Sbjct: 186 LLV 188
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 11/83 (13%)
Query: 218 GPPSKILWVGYPPSVQMDEQML--HNAMILFGEIERIKSYP--------SRNYSFVEFRS 267
G ++ L+VG P +E M+ NA + G + + P +N++F+EFRS
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 268 VDEARRAKEGLQGRLFNDPRITI 290
VDE +A G +F + I
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKI 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 33/95 (34%), Positives = 53/95 (55%), Gaps = 9/95 (9%)
Query: 94 AKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAA 147
A + L+VGG+++ V + L F+ FG+I D + D T AFVE+ EDAA
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 148 EALKNINGRQIGGEQLRVDFLRSQPSR-REQWPNS 181
A+ N+N ++ G +RV+ ++P R +E P+S
Sbjct: 69 AAIDNMNESELFGRTIRVNL--AKPMRIKESGPSS 101
Score = 46.2 bits (108), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAAKDAL 76
L+VG L+ + D L F FG + + T R FAFV F+ EDA AA D +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 77 QGSDFRGNPIKIEFARPAK 95
S+ G I++ A+P +
Sbjct: 75 NESELFGRTIRVNLAKPMR 93
Score = 33.9 bits (76), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 8/69 (11%)
Query: 222 KILWVGYPPSVQMDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAK 275
++L+VG + ++D+++LH A I FG+I I+ + R ++FVEF ++A A
Sbjct: 13 RVLYVG-GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 276 EGL-QGRLF 283
+ + + LF
Sbjct: 72 DNMNESELF 80
>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 = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 37/171 (21%), Positives = 75/171 (43%), Gaps = 26/171 (15%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAAKD 74
++VG++ + + +++ F FG + + T + FAFV ++ E A+ A +
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 75 ALQGSDFRGNPIKI--------------EFARPAKPSKHLWVGGISQTVSKEELEEGFLK 120
G IK+ + A A+ ++V + Q +S ++++ F
Sbjct: 73 QXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 132
Query: 121 FGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRV 165
FG I+ +D T F+EY + + + +A+ + N +GG+ LRV
Sbjct: 133 FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
Score = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/80 (20%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 15 KEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVED 68
+EA + ++V ++ D +D D+K +F FG + TT + + F+ +++ +
Sbjct: 104 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 163
Query: 69 AKAAKDALQGSDFRGNPIKI 88
++ A + D G +++
Sbjct: 164 SQDAVSSXNLFDLGGQYLRV 183
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 52.8 bits (125), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 33/87 (37%), Positives = 46/87 (52%), Gaps = 7/87 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT-----TYSSRSFAFVYFKRVEDAK 70
EA L++G L+ +T + LK +FGK G + +V T SR FAF+ F+ DAK
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62
Query: 71 AAKDALQGSDFRGNPIKIEFARPAKPS 97
A + G G IK+E A+ KPS
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAK--KPS 87
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 42/72 (58%), Gaps = 5/72 (6%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT-----AFVEYSRLEDAAEALKNIN 154
L++GG+++ +++ L+ F K G I + +KD + AF+ + DA A K++N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 155 GRQIGGEQLRVD 166
G+ + G+ ++V+
Sbjct: 70 GKSLHGKAIKVE 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 = 52.0 bits (123), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 94 AKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAA 147
A + L+VGG+++ V + L F+ FG+I D + D T AFVE+ EDAA
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 148 EALKNINGRQIGGEQLRVDFLR 169
A+ N+N ++ G +RV+ +
Sbjct: 64 AAIDNMNESELFGRTIRVNLAK 85
Score = 43.5 bits (101), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKDAL 76
L+VG L+ + D L F FG + + T R FAFV F+ EDA AA D +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 77 QGSDFRGNPIKIEFAR 92
S+ G I++ A+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 32.7 bits (73), Expect = 1.1, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 8/69 (11%)
Query: 222 KILWVGYPPSVQMDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAK 275
++L+VG + ++D+++LH A I FG+I I+ + R ++FVEF ++A A
Sbjct: 8 RVLYVG-GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
Query: 276 EGL-QGRLF 283
+ + + LF
Sbjct: 67 DNMNESELF 75
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 52.0 bits (123), Expect = 2e-06, Method: Composition-based stats.
Identities = 45/152 (29%), Positives = 79/152 (51%), Gaps = 13/152 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLK----ELFGKFG-ALDKVTTYSSRSFAFVYFKRVEDAK 70
E+ NL++GNL+ + + A+LK ELF K A+ V T ++R F +V F+ ED +
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 68
Query: 71 AAKDALQGSDFRGNPIKIEF-----ARPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIE 125
A + L G GN IK+E ++ + ++ L +S ++++EL+E F +E
Sbjct: 69 KALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFED--ALE 125
Query: 126 DFKFLKDGNTAFVEYSRLEDAAEALKNINGRQ 157
+DG + + Y + A+A KN+ +Q
Sbjct: 126 IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 157
Score = 32.7 bits (73), Expect = 1.0, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 10 RAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTT-YSSRSFAFVYFKRVED 68
+ D K+ + L NLS + T+ +LKE+F + V+ S+ A++ FK D
Sbjct: 89 KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD 148
Query: 69 AKAAKDALQGSDFRGNPIKIEF 90
A+ + QG++ G + + +
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYY 170
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 52.0 bits (123), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 94 AKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAA 147
A + L+VGG+++ V + L F+ FG+I D + D T AFVE+ EDAA
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 148 EALKNINGRQIGGEQLRVDF 167
A+ N+N ++ G +RV+
Sbjct: 120 AAIDNMNESELFGRTIRVNL 139
Score = 42.7 bits (99), Expect = 8e-04, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKDAL 76
L+VG L+ + D L F FG + + T R FAFV F+ EDA AA D +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 77 QGSDFRGNPIKIEFA 91
S+ G I++ A
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 32.7 bits (73), Expect = 0.92, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 8/69 (11%)
Query: 222 KILWVGYPPSVQMDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAK 275
++L+VG + ++D+++LH A I FG+I I+ + R ++FVEF ++A A
Sbjct: 64 RVLYVG-GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 276 EGL-QGRLF 283
+ + + LF
Sbjct: 123 DNMNESELF 131
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 6/76 (7%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNI 153
L+VGG+++ V + L F+ FG+I D + D T AFVE+ EDAA A+ N+
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 154 NGRQIGGEQLRVDFLR 169
N ++ G +RV+ +
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 43.5 bits (101), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKDAL 76
L+VG L+ + D L F FG + + T R FAFV F+ EDA AA D +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 77 QGSDFRGNPIKIEFAR 92
S+ G I++ A+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 8/69 (11%)
Query: 222 KILWVGYPPSVQMDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAK 275
++L+VG + ++D+++LH A I FG+I I+ + R ++FVEF ++A A
Sbjct: 6 RVLYVG-GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64
Query: 276 EGL-QGRLF 283
+ + + LF
Sbjct: 65 DNMNESELF 73
>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 = 51.2 bits (121), Expect = 3e-06, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNI 153
L+VGG+++ V + L F+ FG+I D + D T AFVE+ EDAA A+ N+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 154 NGRQIGGEQLRVDF 167
N ++ G +RV+
Sbjct: 65 NESELFGRTIRVNL 78
Score = 42.7 bits (99), Expect = 0.001, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKDAL 76
L+VG L+ + D L F FG + + T R FAFV F+ EDA AA D +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 77 QGSDFRGNPIKIEFA 91
S+ G I++ A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 32.7 bits (73), Expect = 1.0, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 8/69 (11%)
Query: 222 KILWVGYPPSVQMDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAK 275
++L+VG + ++D+++LH A I FG+I I+ + R ++FVEF ++A A
Sbjct: 3 RVLYVG-GLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 61
Query: 276 EGL-QGRLF 283
+ + + LF
Sbjct: 62 DNMNESELF 70
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 51.2 bits (121), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 41/132 (31%), Positives = 60/132 (45%), Gaps = 14/132 (10%)
Query: 15 KEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVED 68
KE L++G LS +TTD L+ F ++G L T SR F FV + VE+
Sbjct: 9 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 68
Query: 69 AKAAKDAL-QGSDFRGNPIKIEFARP--AKPSKHL-----WVGGISQTVSKEELEEGFLK 120
AA +A D R K +R +P HL +VGGI + + L + F +
Sbjct: 69 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 128
Query: 121 FGNIEDFKFLKD 132
+G IE + + D
Sbjct: 129 YGKIEVIEIMTD 140
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 50.8 bits (120), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 75/155 (48%), Gaps = 20/155 (12%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS--------FAFVYFKRVEDAKAAKD 74
++VG + ++ DL+ELF ++GA+ ++ RS FV F + A A++
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 75 ALQGSDF---RGNPIKIEFARPAK----PSKHLWVGGISQTVSKEELEEGFLKFGNIEDF 127
AL +PI+++ A K + L++G IS+ ++ ++ F FG IE+
Sbjct: 78 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 137
Query: 128 KFLK--DG---NTAFVEYSRLEDAAEALKNINGRQ 157
+ L+ DG AFV ++ A A+K ++ Q
Sbjct: 138 RILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ 172
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 50.4 bits (119), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 75/155 (48%), Gaps = 20/155 (12%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS--------FAFVYFKRVEDAKAAKD 74
++VG + ++ DL+ELF ++GA+ ++ RS FV F + A A++
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 75 ALQGSDF---RGNPIKIEFARPAK----PSKHLWVGGISQTVSKEELEEGFLKFGNIEDF 127
AL +PI+++ A K + L++G IS+ ++ ++ F FG IE+
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 128 KFLK--DG---NTAFVEYSRLEDAAEALKNINGRQ 157
+ L+ DG AFV ++ A A+K ++ Q
Sbjct: 126 RILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ 160
>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 = 50.1 bits (118), Expect = 6e-06, Method: Composition-based stats.
Identities = 41/132 (31%), Positives = 60/132 (45%), Gaps = 14/132 (10%)
Query: 15 KEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVED 68
KE L++G LS +TTD L+ F ++G L T SR F FV + VE+
Sbjct: 1 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Query: 69 AKAAKDAL-QGSDFRGNPIKIEFAR--PAKPSKHL-----WVGGISQTVSKEELEEGFLK 120
AA +A D R K +R +P HL +VGGI + + L + F +
Sbjct: 61 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120
Query: 121 FGNIEDFKFLKD 132
+G IE + + D
Sbjct: 121 YGKIEVIEIMTD 132
>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 = 50.1 bits (118), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 6/76 (7%)
Query: 22 NLWVGNLSADTTDADLKELFGKF------GALDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
NL+VG+L+ + D L+ F F + + T SSR + FV F +DA+ A D+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 76 LQGSDFRGNPIKIEFA 91
+QG D G P++I +A
Sbjct: 63 MQGQDLNGRPLRINWA 78
Score = 32.3 bits (72), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 7/67 (10%)
Query: 224 LWVGYPPSVQMDEQMLHNAM-----ILFGEIER-IKSYPSRNYSFVEFRSVDEARRAKEG 277
L+VG +V +D++ L NA L G + +++ SR Y FV F S D+A+ A +
Sbjct: 4 LFVG-DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 278 LQGRLFN 284
+QG+ N
Sbjct: 63 MQGQDLN 69
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALKN 152
+L+VG ++ V E L F F + + D T FV ++ +DA A+ +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 153 INGRQIGGEQLRVDF 167
+ G+ + G LR+++
Sbjct: 63 MQGQDLNGRPLRINW 77
>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 = 49.7 bits (117), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 51/99 (51%), Gaps = 6/99 (6%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALKN 152
H++VG +S ++ E+++ F FG I D + +KD T FV + DA A++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 153 INGRQIGGEQLRVDFLRSQPSRREQWPNSHDARDGPIIG 191
+ G+ +GG Q+R ++ +P + S+ + GP G
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115
Score = 33.9 bits (76), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 22 NLWVGNLSADTTDADLKELFGKFG------ALDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
+++VG+LS + T D+K F FG + + T S+ + FV F DA+ A
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 76 LQGSDFRGNPIKIEFARPAKPS 97
+ G G I+ +A P+
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPA 98
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 49.7 bits (117), Expect = 8e-06, Method: Composition-based stats.
Identities = 41/138 (29%), Positives = 63/138 (45%), Gaps = 14/138 (10%)
Query: 9 NRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVY 62
+++ KE L++G LS +TTD L+ F ++G L T SR F FV
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 63 FKRVEDAKAAKDAL-QGSDFRGNPIKIEFAR--PAKPSKHL-----WVGGISQTVSKEEL 114
+ VE+ AA +A D R K +R +P HL +VGGI + + L
Sbjct: 62 YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 121
Query: 115 EEGFLKFGNIEDFKFLKD 132
+ F ++G IE + + D
Sbjct: 122 RDYFEQYGKIEVIEIMTD 139
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 49.7 bits (117), Expect = 8e-06, Method: Composition-based stats.
Identities = 41/132 (31%), Positives = 60/132 (45%), Gaps = 14/132 (10%)
Query: 15 KEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVED 68
KE L++G LS +TTD L+ F ++G L T SR F FV + VE+
Sbjct: 6 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 65
Query: 69 AKAAKDAL-QGSDFRGNPIKIEFAR--PAKPSKHL-----WVGGISQTVSKEELEEGFLK 120
AA +A D R K +R +P HL +VGGI + + L + F +
Sbjct: 66 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 125
Query: 121 FGNIEDFKFLKD 132
+G IE + + D
Sbjct: 126 YGKIEVIEIMTD 137
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 49.7 bits (117), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 92 RPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALK 151
R + L+V G + ++ L F FGNI D N AFV Y ++E A +A+
Sbjct: 10 RAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVA 67
Query: 152 NINGRQIGGEQLRVDFLRSQP 172
+NG Q+ QL+V+ R QP
Sbjct: 68 ELNGTQVESVQLKVNIARKQP 88
Score = 33.5 bits (75), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 14 DKEAPPSSN-LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAA 72
++ AP N L+V D T L+ F FG + ++ R+ AFV ++++E A A
Sbjct: 8 ERRAPRKGNTLYV--YGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQA 65
Query: 73 KDALQGSDFRGNPIKIEFAR 92
L G+ +K+ AR
Sbjct: 66 VAELNGTQVESVQLKVNIAR 85
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 49.7 bits (117), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 92 RPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALK 151
R + L+V G + ++ L F FGNI D N AFV Y ++E A +A+
Sbjct: 34 RAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVA 91
Query: 152 NINGRQIGGEQLRVDFLRSQP 172
+NG Q+ QL+V+ R QP
Sbjct: 92 ELNGTQVESVQLKVNIARKQP 112
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 5 PSKFNRAYDDKEAPPSSN-LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYF 63
P + + ++ ++ AP N L+V D T L+ F FG + ++ R+ AFV +
Sbjct: 23 PFRRSDSFPERRAPRKGNTLYV--YGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTY 80
Query: 64 KRVEDAKAAKDALQGSDFRGNPIKIEFAR 92
+++E A A L G+ +K+ AR
Sbjct: 81 EKMESADQAVAELNGTQVESVQLKVNIAR 109
>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 = 49.7 bits (117), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 6/82 (7%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKD 74
++L V NL+ T+ L+ +F K+G + V T SR FAFV F DA+ A D
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 75 ALQGSDFRGNPIKIEFARPAKP 96
A+ G+ G ++++ AR +P
Sbjct: 108 AMDGAVLDGRELRVQMARYGRP 129
Score = 37.0 bits (84), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 11/89 (12%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNI 153
L V ++ S + L F K+G + D +D T AFV + DA +A+ +
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 154 NGRQIGGEQLRVDFLRSQPSRREQWPNSH 182
+G + G +LRV Q +R + P+SH
Sbjct: 110 DGAVLDGRELRV-----QMARYGRPPDSH 133
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 49.3 bits (116), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKN 152
H++VG +S ++ E+++ F FG I D + +KD T FV + DA A+ +
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 153 INGRQIGGEQLRVDFLRSQP 172
+ G+ +GG Q+R ++ +P
Sbjct: 77 MGGQWLGGRQIRTNWATRKP 96
Score = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 22 NLWVGNLSADTTDADLKELFGKFGALD------KVTTYSSRSFAFVYFKRVEDAKAAKDA 75
+++VG+LS + T D+K F FG + + T S+ + FV F DA+ A
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 76 LQGSDFRGNPIKIEFA--RPAKPS 97
+ G G I+ +A +P PS
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPS 100
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 49.3 bits (116), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 6/85 (7%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALK 151
+ ++VG I ++E+L++ F + G + F+ + D T F EY E A A++
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 152 NINGRQIGGEQLRVDFLRSQPSRRE 176
N+NGR+ G LRVD S+ ++ E
Sbjct: 69 NLNGREFSGRALRVDNAASEKNKEE 93
Score = 33.1 bits (74), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 22 NLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS------FAFVYFKRVEDAKAAKDA 75
+++VGN+ + T+ LK++F + G + R + F ++ E A +A
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 76 LQGSDFRGNPIKIEFARPAKPSKHL 100
L G +F G ++++ A K + L
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEEL 94
>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 = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 41/138 (29%), Positives = 63/138 (45%), Gaps = 14/138 (10%)
Query: 9 NRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVY 62
+++ KE L++G LS +TTD L+ F ++G L T SR F FV
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 63 FKRVEDAKAAKDAL-QGSDFRGNPIKIEFAR--PAKPSKHL-----WVGGISQTVSKEEL 114
+ VE+ AA +A D R K +R +P HL +VGGI + + L
Sbjct: 62 YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 121
Query: 115 EEGFLKFGNIEDFKFLKD 132
+ F ++G IE + + D
Sbjct: 122 RDYFEQYGKIEVIEIMTD 139
>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 = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 41/138 (29%), Positives = 63/138 (45%), Gaps = 14/138 (10%)
Query: 9 NRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVY 62
+++ KE L++G LS +TTD L+ F ++G L T SR F FV
Sbjct: 1 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 60
Query: 63 FKRVEDAKAAKDAL-QGSDFRGNPIKIEFAR--PAKPSKHL-----WVGGISQTVSKEEL 114
+ VE+ AA +A D R K +R +P HL +VGGI + + L
Sbjct: 61 YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 120
Query: 115 EEGFLKFGNIEDFKFLKD 132
+ F ++G IE + + D
Sbjct: 121 RDYFEQYGKIEVIEIMTD 138
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 47.0 bits (110), Expect = 5e-05, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 6/82 (7%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKD 74
++L V NL+ T+ L+ +F K+G + V T SR FAFV F DA+ A D
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 75 ALQGSDFRGNPIKIEFARPAKP 96
A+ G+ G ++++ AR +P
Sbjct: 131 AMDGAVLDGRELRVQMARYGRP 152
Score = 34.3 bits (77), Expect = 0.37, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 11/89 (12%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNI 153
L V ++ S + L F K+G + D +D T AFV + DA +A+ +
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 154 NGRQIGGEQLRVDFLRSQPSRREQWPNSH 182
+G + G +LRV Q +R + P+SH
Sbjct: 133 DGAVLDGRELRV-----QMARYGRPPDSH 156
>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 = 47.0 bits (110), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSR-SFAFVYFKRVEDAKAAKD 74
E PP+ L++ NL +T + L LF +F +V R AFV F A AA+D
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARD 262
Query: 75 ALQGSDF-RGNPIKIEFAR 92
ALQG + N +KI FA+
Sbjct: 263 ALQGFKITQNNAMKISFAK 281
Score = 43.9 bits (102), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFGALDKVTTYSS---RSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG + + S R AFV FK V
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAK 88
Score = 29.6 bits (65), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 217 DGPPSKILWVGYPPSVQMDEQMLHNAMILFGEIERIKSYPSR-NYSFVEFRSVDEARRAK 275
+ PP+ IL++ P + +E ML F + ++ P R + +FVEF + +A A+
Sbjct: 203 ENPPNHILFLTNLPE-ETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 261
Query: 276 EGLQG 280
+ LQG
Sbjct: 262 DALQG 266
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 47.0 bits (110), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 95 KPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNIN 154
K S L VG IS T + +EL F ++G + + +KD AFV R EDA EA++ ++
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--YAFVHMERAEDAVEAIRGLD 65
Query: 155 GRQIGGEQLRVDFLRSQ 171
+ G+++ V S+
Sbjct: 66 NTEFQGKRMHVQLSTSR 82
Score = 43.1 bits (100), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQGS 79
S+ L VGN+S T+ +L+ F ++G + + + +AFV+ +R EDA A L +
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNT 67
Query: 80 DFRGNPIKIEFA 91
+F+G + ++ +
Sbjct: 68 EFQGKRMHVQLS 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 = 46.6 bits (109), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 39/71 (54%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQGSD 80
S L+VGNL D T+ ++++LF K+G +V + + F F+ + A+ AK L
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 75
Query: 81 FRGNPIKIEFA 91
RG +++ FA
Sbjct: 76 LRGKQLRVRFA 86
Score = 31.2 bits (69), Expect = 3.1, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 33/68 (48%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNINGRQIG 159
L+VG + +++EE+ + F K+G + KD F+ A A ++ +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 77
Query: 160 GEQLRVDF 167
G+QLRV F
Sbjct: 78 GKQLRVRF 85
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 46.2 bits (108), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQGS 79
++ L+V D +++L E+FG FG + +V + FAFV F+ E A A + + G
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--GFAFVEFEEAESAAKAIEEVHGK 88
Query: 80 DFRGNPIKIEFAR-PAK 95
F P+++ +++ PAK
Sbjct: 89 SFANQPLEVVYSKLPAK 105
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 46.2 bits (108), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSR-SFAFVYFKRVEDAKAAKD 74
E PP+ L++ NL +T + L LF +F +V R AFV F A AA+D
Sbjct: 9 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARD 68
Query: 75 ALQGSDF-RGNPIKIEFAR 92
ALQG + N +KI FA+
Sbjct: 69 ALQGFKITQNNAMKISFAK 87
Score = 30.4 bits (67), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 217 DGPPSKILWVGYPPSVQMDEQMLHNAMILFGEIERIKSYPSR-NYSFVEFRSVDEARRAK 275
+ PP+ IL++ P + +E ML F + ++ P R + +FVEF + +A A+
Sbjct: 9 ENPPNHILFLTNLPE-ETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAAR 67
Query: 276 EGLQG 280
+ LQG
Sbjct: 68 DALQG 72
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 4/74 (5%)
Query: 23 LWVGNLSADTTDADLKELFGKF--GALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQGSD 80
L+V NL T++ +++ F GA+++V R +AFV+F EDA A AL G
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKV 75
Query: 81 FRGNPIKIEFARPA 94
G+PI++ A+P
Sbjct: 76 LDGSPIEVTLAKPV 89
Score = 43.1 bits (100), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 4/74 (5%)
Query: 98 KHLWVGGISQTVSKEELEEGF--LKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNING 155
K L+V + + S+E +E+ F +K G +E K ++D AFV +S EDA EA+K +NG
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--YAFVHFSNREDAVEAMKALNG 73
Query: 156 RQIGGEQLRVDFLR 169
+ + G + V +
Sbjct: 74 KVLDGSPIEVTLAK 87
Score = 33.1 bits (74), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 222 KILWVG---YPPSVQMDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGL 278
KIL+V S +M E+ +N I G +ER+K R+Y+FV F + ++A A + L
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNN--IKPGAVERVKKI--RDYAFVHFSNREDAVEAMKAL 71
Query: 279 QGRLFNDPRITIMFS 293
G++ + I + +
Sbjct: 72 NGKVLDGSPIEVTLA 86
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS-----FAFVYFKRVEDAKAAKDA 75
+ L V NL +DAD++ELF +FG L K RS A V+F+R DA A
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148
Query: 76 LQGSDFRGNPIKIEFA 91
+G G P+ I+
Sbjct: 149 YKGVPLDGRPMDIQLV 164
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 44.3 bits (103), Expect = 4e-04, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS---FAFVYFKRVEDAKAAKDALQGS 79
++VGNL D D++++F K+GA+ + + R FAFV F+ DA+ A G
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 80 DFRGNPIKIEFARPAK 95
D+ G +++EF R +
Sbjct: 85 DYDGYRLRVEFPRSGR 100
Score = 36.6 bits (83), Expect = 0.061, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIED--FKFLKDGNT-AFVEYSRLEDAAEALKNINGR 156
++VG + + +++E+ F K+G I D K + G AFVE+ DA +A+ +G
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 157 QIGGEQLRVDFLRS 170
G +LRV+F RS
Sbjct: 85 DYDGYRLRVEFPRS 98
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS-----FAFVYFKRVEDAKAAKDALQ 77
L V NL +DAD++ELF +FG L K + RS A V+F+R DA A
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 78 GSDFRGNPIKIEFA 91
G G P+ I+
Sbjct: 91 GVPLDGRPMNIQLV 104
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGN-----TAFVEYSRLEDAAEALKNIN 154
L V + VS +++E F +FG ++ D + TA V + R DA +A+K N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 155 GRQIGGEQLRVDFLRS 170
G + G + + + S
Sbjct: 91 GVPLDGRPMNIQLVTS 106
>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 = 43.5 bits (101), Expect = 5e-04, Method: Composition-based stats.
Identities = 40/148 (27%), Positives = 70/148 (47%), Gaps = 20/148 (13%)
Query: 24 WVGNLSADTTDADLKELFGKFGALDKVTTYSSRS--------FAFVYFKRVEDAKAAKDA 75
+VG + ++ DL+ELF ++GA+ ++ RS FV F + A A++A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 76 LQGSDF---RGNPIKIEFARPAK----PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFK 128
L +PI+ + A K + L++G IS+ ++ ++ F FG IE+ +
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECR 126
Query: 129 FLK--DG---NTAFVEYSRLEDAAEALK 151
L+ DG AFV ++ A A+K
Sbjct: 127 ILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 43.5 bits (101), Expect = 6e-04, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 20 SSNLW---VGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDAL 76
S N W VGN+SA T +L+ LF + G + + + +AFV+ ++ DAKAA L
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQL 63
Query: 77 QGSDFRGNPIKIEFA 91
G + +G I +E +
Sbjct: 64 NGKEVKGKRINVELS 78
Score = 38.5 bits (88), Expect = 0.018, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 4/82 (4%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNINGRQIG 159
++VG +S + +EL F + G + + +KD AFV + DA A+ +NG+++
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--YAFVHMEKEADAKAAIAQLNGKEVK 69
Query: 160 GEQLRVDFLRSQPSRREQWPNS 181
G+++ V+ S +++ P+S
Sbjct: 70 GKRINVEL--STKGQKKSGPSS 89
>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 = 43.1 bits (100), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS-----FAFVYFKRVEDAKAAKDALQ 77
L V NL +DAD++ELF +FG L K + RS A V+F+R DA A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 78 GSDFRGNPIKIEFA 91
G G P I+
Sbjct: 92 GVPLDGRPXNIQLV 105
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 43.1 bits (100), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 39/73 (53%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNINGRQIG 159
++ GGI+ ++ + + + F FG I + + + +FV +S E AA A+ ++NG I
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIE 87
Query: 160 GEQLRVDFLRSQP 172
G ++ + + P
Sbjct: 88 GHVVKCYWGKESP 100
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 42/79 (53%)
Query: 14 DKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAK 73
++ +P + ++ G +++ TD +++ F FG + ++ + + ++FV F E A A
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAI 78
Query: 74 DALQGSDFRGNPIKIEFAR 92
++ G+ G+ +K + +
Sbjct: 79 VSVNGTTIEGHVVKCYWGK 97
Score = 35.4 bits (80), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 215 NRDGPPSKILWVGYPPSVQMDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRA 274
N+ P + ++ G S + +Q++ FG+I I+ +P + YSFV F + + A A
Sbjct: 19 NQSSPKNCTVYCGGIAS-GLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHA 77
Query: 275 KEGLQG 280
+ G
Sbjct: 78 IVSVNG 83
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS-----FAFVYFKRVEDAKAAKDA 75
+ L V NL +DAD++ELF +FG L K RS A V+F+R DA A
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 76 LQGSDFRGNPIKIEF 90
+G G P+ I+
Sbjct: 96 YKGVPLDGRPMDIQL 110
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS-----FAFVYFKRVEDAKAAKDA 75
+ L V NL +DAD++ELF +FG L K RS A V+F+R DA A
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 76 LQGSDFRGNPIKIEF 90
+G G P+ I+
Sbjct: 96 YKGVPLDGRPMDIQL 110
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 22 NLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKDA 75
L V NL+ T+ L+ +F K+G + V T + R FAFV F DA+ A+ A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 76 LQGSDFRGNPIKIEFAR 92
+ G++ G ++++ AR
Sbjct: 75 MDGAELDGRELRVQVAR 91
Score = 33.1 bits (74), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNI 153
L V ++ S + L F K+G + D ++ +T AFV + DA +A +
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 154 NGRQIGGEQLRVDFLR 169
+G ++ G +LRV R
Sbjct: 76 DGAELDGRELRVQVAR 91
>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 = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAK 73
SS L+VG+L + T+ L+ +F FG +D + T S+ + F+ F E A+ A
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 74 DALQGSDFRGNPIKI 88
+ L G + G P+++
Sbjct: 65 EQLNGFELAGRPMRV 79
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 97 SKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEAL 150
S L+VG + ++++ L F FG I++ +KD +T F+ +S E A AL
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 151 KNINGRQIGGEQLRV 165
+ +NG ++ G +RV
Sbjct: 65 EQLNGFELAGRPMRV 79
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 42.7 bits (99), Expect = 0.001, Method: Composition-based stats.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 10/88 (11%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRS---------FAFVYFKRVEDAK 70
SS L++ NL+ TT+ LK +F K GA+ T ++ F FV +K+ E A+
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 71 AAKDALQGSDFRGNPIKIEFA-RPAKPS 97
A LQG G+ +++ + R KP+
Sbjct: 65 KALKQLQGHTVDGHKLEVRISERATKPA 92
Score = 34.7 bits (78), Expect = 0.23, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 9/78 (11%)
Query: 97 SKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA---------FVEYSRLEDAA 147
S L++ ++ + ++E L+ F K G I+ K N A FVEY + E A
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 148 EALKNINGRQIGGEQLRV 165
+ALK + G + G +L V
Sbjct: 65 KALKQLQGHTVDGHKLEV 82
>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 = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 61
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 62 ATNALRSMQGFPFYDKPMRIQYAK 85
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAK 87
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 96 PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEA 149
PS+ +++G I ++E++ + G + + K + D T AF+E+ LE +A A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 150 LKNINGRQIGGEQLRVDF 167
++N+NG Q+G L+ +
Sbjct: 63 VRNLNGYQLGSRFLKCGY 80
Score = 33.9 bits (76), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 219 PPSKILWVGYPPSVQMDEQMLH---------NAMILFGEIERIKSYPSRNYSFVEFRSVD 269
PPS+++++G P Q +EQ+L N ++F ++ S+ Y+F+EFR ++
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP----QTGRSKGYAFIEFRDLE 57
Query: 270 EARRAKEGLQG 280
+ A L G
Sbjct: 58 SSASAVRNLNG 68
>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 = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 25/59 (42%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 23 LWVGNLSADTTDADLKELFGKFG-------ALDKVTTYSSRSFAFVYFKRVEDAKAAKD 74
+++G LS DTT DLK+ F KFG LD +T SR F FV FK E D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITG-RSRGFGFVLFKESESVDKVMD 59
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
Length = 101
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQGS 79
++ L+V D +++L E+FG FG + +V + FAFV F+ E A A + + G
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--GFAFVEFEEAESAAKAIEEVHGK 61
Query: 80 DFRGNPIKIEFAR 92
F P+++ +++
Sbjct: 62 SFANQPLEVVYSK 74
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 97 SKHLWVGGISQTVSKEELEEGFLK--FGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNIN 154
SK L + +S + ++E L+E F K F + + K AF+E++ EDA EAL + N
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 155 GRQIGGEQLRVDF 167
R+I G +R++
Sbjct: 75 KREIEGRAIRLEL 87
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 20 SSNLWVGNLSADTTDADLKELFGK--FGALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQ 77
S L + NLS T+ L+E+F K F + + S+ +AF+ F EDAK A ++
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 78 GSDFRGNPIKIEFARP 93
+ G I++E P
Sbjct: 75 KREIEGRAIRLELQGP 90
>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 = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFGALDKVTTYSS---RSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG + + S R AFV FK V
Sbjct: 1 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 60
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 61 ATNALRSMQGFPFYDKPMRIQYAK 84
Score = 29.6 bits (65), Expect = 8.2, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 232 VQMDE--QMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDP 286
++ DE + LH FG+I I +S R +FV F+ V A A +QG F D
Sbjct: 17 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 76
Query: 287 RITIMFSSSE 296
+ I ++ ++
Sbjct: 77 PMRIQYAKTD 86
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 45/81 (55%), Gaps = 8/81 (9%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAF------VEYSRLEDAAEALKNI 153
L+V G+ + ++E++ + F ++G I++ D T + VEY ++A A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 154 NGRQIGGEQLRVD--FLRSQP 172
NG+ + G+ + VD F+R P
Sbjct: 70 NGQDLMGQPISVDWCFVRGPP 90
Score = 37.7 bits (86), Expect = 0.032, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 23 LWVGNLSADTTDADLKELFGKFGA-------LDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
L+V + + T+ D+ + F ++G LD+ T Y + + V ++ ++A+AA +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL-KGYTLVEYETYKEAQAAMEG 68
Query: 76 LQGSDFRGNPIKIEF 90
L G D G PI +++
Sbjct: 69 LNGQDLMGQPISVDW 83
Score = 30.4 bits (67), Expect = 4.6, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 225 WVGYPPSVQMD--EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKE 276
W+ + V + E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A E
Sbjct: 8 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 277 GLQGR 281
GL G+
Sbjct: 68 GLNGQ 72
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 42.0 bits (97), Expect = 0.002, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 37/80 (46%), Gaps = 7/80 (8%)
Query: 22 NLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKDA 75
N++VGNL T +KELF +FG + V T + F FV + E A
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 76 LQGSDFRGNPIKIEFARPAK 95
L +DF G I++ A P K
Sbjct: 62 LDNTDFMGRTIRVTEANPKK 81
Score = 33.1 bits (74), Expect = 0.82, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 7/74 (9%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALK 151
++++VG + + + E+++E F +FG + + K + D T FVE E +EA+
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60
Query: 152 NINGRQIGGEQLRV 165
++ G +RV
Sbjct: 61 KLDNTDFMGRTIRV 74
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTY----SSRSFAFVYFKRVEDAKAAKDALQG 78
L V N+ D DL+++FG+FG + V S+ F FV F+ DA A++ L G
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
Query: 79 SDFRGNPIKI 88
+ G I++
Sbjct: 92 TVVEGRKIEV 101
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 17 APPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAK 70
AP S ++V NL T+ DL +F K+G + KVT T S+ AF+ F + A+
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 71 AAKDALQGSDFRGNPIKIEFA 91
A+ G IK A
Sbjct: 73 NCTRAINNKQLFGRVIKASIA 93
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 96 PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEA 149
PS+ +++G I ++E++ + G + + K + D T AF+E+ LE +A A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 150 LKNINGRQIGGEQLRVDF 167
++N+NG Q+G L+ +
Sbjct: 62 VRNLNGYQLGSRFLKCGY 79
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 13/70 (18%)
Query: 220 PSKILWVGYPPSVQMDEQMLH---------NAMILFGEIERIKSYPSRNYSFVEFRSVDE 270
PS+++++G P Q +EQ+L N ++F ++ S+ Y+F+EFR ++
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP----QTGRSKGYAFIEFRDLES 57
Query: 271 ARRAKEGLQG 280
+ A L G
Sbjct: 58 SASAVRNLNG 67
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A ++QG F P++I++A+
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 96 PSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEA 149
PS+ +++G I ++E++ + G + + K + D T AF+E+ LE +A A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 150 LKNINGRQIGGEQLRVDF 167
++N+NG Q+G L+ +
Sbjct: 61 VRNLNGYQLGSRFLKCGY 78
Score = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 13/70 (18%)
Query: 220 PSKILWVGYPPSVQMDEQMLH---------NAMILFGEIERIKSYPSRNYSFVEFRSVDE 270
PS+++++G P Q +EQ+L N ++F ++ S+ Y+F+EFR ++
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP----QTGRSKGYAFIEFRDLES 56
Query: 271 ARRAKEGLQG 280
+ A L G
Sbjct: 57 SASAVRNLNG 66
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTY----SSRSFAFVYFKRVEDAKAAKDALQG 78
L V N+ D DL+++FG+FG + V S+ F FV F+ DA A++ L G
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 77
Query: 79 SDFRGNPIKI 88
+ G I++
Sbjct: 78 TVVEGRKIEV 87
>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 = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 18 PPSSNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAK 70
P +NL V L + T +L+ LF G + DKV +S + FV + +DA+
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHS-LGYGFVNYVTAKDAE 60
Query: 71 AAKDALQGSDFRGNPIKIEFARPA 94
A + L G + IK+ +ARP+
Sbjct: 61 RAINTLNGLRLQSKTIKVSYARPS 84
Score = 37.7 bits (86), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKD---GNT---AFVEYSRLEDAAEALKN 152
+L V + Q ++++EL F G +E K ++D G++ FV Y +DA A+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 153 INGRQIGGEQLRVDFLR 169
+NG ++ + ++V + R
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
>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 = 41.2 bits (95), Expect = 0.003, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 45/81 (55%), Gaps = 8/81 (9%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAF------VEYSRLEDAAEALKNI 153
L+V G+ + ++E++ + F ++G I++ D T + VEY ++A A++ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 154 NGRQIGGEQLRVD--FLRSQP 172
NG+ + G+ + VD F+R P
Sbjct: 86 NGQDLMGQPISVDWCFVRGPP 106
Score = 37.0 bits (84), Expect = 0.058, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 23 LWVGNLSADTTDADLKELFGKFGA-------LDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
L+V + + T+ D+ + F ++G LD+ T Y + + V ++ ++A+AA +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL-KGYTLVEYETYKEAQAAMEG 84
Query: 76 LQGSDFRGNPIKIEF 90
L G D G PI +++
Sbjct: 85 LNGQDLMGQPISVDW 99
Score = 30.0 bits (66), Expect = 6.6, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 11/82 (13%)
Query: 211 SVGRNRDGP-PSKIL--WVGYPPSVQMD--EQMLHNAMILFGEIERI------KSYPSRN 259
SV ++ D P P + + W+ + V + E+ +H+ +GEI+ I ++ +
Sbjct: 7 SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66
Query: 260 YSFVEFRSVDEARRAKEGLQGR 281
Y+ VE+ + EA+ A EGL G+
Sbjct: 67 YTLVEYETYKEAQAAMEGLNGQ 88
>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 = 41.2 bits (95), Expect = 0.003, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAF------VEYSRLEDAAEALKNI 153
L+V G+ + ++E++ + F ++G I++ D T + VEY ++A A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 154 NGRQIGGEQLRVDF 167
NG+ + G+ + VD+
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 38.9 bits (89), Expect = 0.015, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 23 LWVGNLSADTTDADLKELFGKFGA-------LDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
L+V + + T+ D+ + F ++G LD+ T Y + + V ++ ++A+AA +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL-KGYTLVEYETYKEAQAAMEG 68
Query: 76 LQGSDFRGNPIKIEF 90
L G D G PI +++
Sbjct: 69 LNGQDLMGQPISVDW 83
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 225 WVGYPPSVQMD--EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKE 276
W+ + V + E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A E
Sbjct: 8 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 277 GLQGR 281
GL G+
Sbjct: 68 GLNGQ 72
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 40.8 bits (94), Expect = 0.004, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNI 153
L++GG+ ++ ++++E FG ++ F +KD T AF EY + +A+ +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 154 NGRQIGGEQLRV 165
NG Q+G ++L V
Sbjct: 64 NGMQLGDKKLLV 75
>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 = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 8/68 (11%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVED 68
E+ +NL+V NL TD L +FGK+G++ DK+T R AFV + + E+
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG-RPRGVAFVRYNKREE 67
Query: 69 AKAAKDAL 76
A+ A AL
Sbjct: 68 AQEAISAL 75
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 9/76 (11%)
Query: 88 IEFARPAKPS---KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFV 138
+ +ARP S +L+V + +T++ ++L+ F K+G+I L+D T AFV
Sbjct: 1 MSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 60
Query: 139 EYSRLEDAAEALKNIN 154
Y++ E+A EA+ +N
Sbjct: 61 RYNKREEAQEAISALN 76
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 5/65 (7%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLK--DGNT---AFVEYSRLEDAAEALKN 152
+ L+VG +++ S++++ F FGNIE+ L+ DGN+ AFV+YS +A A+
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 153 INGRQ 157
++G Q
Sbjct: 76 LHGSQ 80
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 15 KEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTY-----SSRSFAFVYFKRVEDA 69
++ P L+VG L+ ++ D++ LF FG +++ T +S+ AFV + +A
Sbjct: 10 RQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEA 69
Query: 70 KAAKDALQGS 79
+AA +AL GS
Sbjct: 70 QAAINALHGS 79
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
Length = 90
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 7/81 (8%)
Query: 19 PSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVEDAKA 71
P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V A
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 72 AKDALQGSDFRGNPIKIEFAR 92
A ++QG F P++I++A+
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAK 82
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 7/81 (8%)
Query: 19 PSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVEDAKA 71
P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V A
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 72 AKDALQGSDFRGNPIKIEFAR 92
A ++QG F P++I++A+
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAK 83
>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 = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 19 PSSNLWVGNLSADTTDADLKE----LFGKFGALDKVT---TYSSRSFAFVYFKRVEDAKA 71
P+ +++ N++ +LK LF +FG + + T R AFV FK + +
Sbjct: 5 PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTN 64
Query: 72 AKDALQGSDFRGNPIKIEFAR 92
A LQG F G P++I++A+
Sbjct: 65 ALRQLQGFPFYGKPMRIQYAK 85
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAF------VEYSRLEDAAEALKNI 153
L+V G+ + ++E++ + F ++G I++ D T + VEY ++A A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 154 NGRQIGGEQLRVDF 167
NG+ + G+ + VD+
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 38.1 bits (87), Expect = 0.022, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 23 LWVGNLSADTTDADLKELFGKFGA-------LDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
L+V + + T+ D+ + F ++G LD+ T Y + + V ++ ++A+AA +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL-KGYTLVEYETYKEAQAAMEG 68
Query: 76 LQGSDFRGNPIKIEF 90
L G D G PI +++
Sbjct: 69 LNGQDLMGQPISVDW 83
Score = 30.8 bits (68), Expect = 3.4, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 225 WVGYPPSVQMD--EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKE 276
W+ + V + E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A E
Sbjct: 8 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 277 GLQGR 281
GL G+
Sbjct: 68 GLNGQ 72
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 30/81 (37%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSR-SFAFVYFKRVEDAKAAKD 74
E PP+ L++ NL +T + L LF +F +V +R AFV F + AAK+
Sbjct: 4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKE 63
Query: 75 ALQGSDFRGNP---IKIEFAR 92
ALQG F+ P +KI FA+
Sbjct: 64 ALQG--FKITPTHAMKITFAK 82
Score = 32.7 bits (73), Expect = 0.96, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 219 PPSKILWVGYPPSVQMDEQMLHNAMILFGEIERIKSYPSR-NYSFVEFRSVDEARRAKEG 277
PP++IL++ P + +E ML F + ++ P+R + +FVEF + ++ AKE
Sbjct: 6 PPNQILFLTNLPE-ETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEA 64
Query: 278 LQG 280
LQG
Sbjct: 65 LQG 67
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 40.4 bits (93), Expect = 0.005, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAKAAK 73
+NL V L + T + K LFG G + DK+T S + FV + DA A
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITG-QSLGYGFVNYSDPNDADKAI 63
Query: 74 DALQGSDFRGNPIKIEFARPAKPS 97
+ L G + IK+ +ARP+ S
Sbjct: 64 NTLNGLKLQTKTIKVSYARPSSAS 87
Score = 37.0 bits (84), Expect = 0.049, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 6/77 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALKN 152
+L V + Q ++++E + F G+IE K ++D T FV YS DA +A+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 153 INGRQIGGEQLRVDFLR 169
+NG ++ + ++V + R
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAAKDAL 76
L+VG+L + T+ L+ +F FG ++ + T S+ + F+ F E AK A + L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 77 QGSDFRGNPIKI 88
G + G P+K+
Sbjct: 89 NGFELAGRPMKV 100
Score = 37.4 bits (85), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNI 153
L+VG + ++++ L F FG IE + + D T F+ +S E A +AL+ +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 154 NGRQIGGEQLRV 165
NG ++ G ++V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 22 NLWVGNLSADTTDADLKELFGKFGALDKVTTY-----SSRSFAFVYFKRVEDAKAAKDAL 76
L+VG L TD D++++F FG +D+ T +S+ AFV F+ +A+AA + L
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 77 QGS 79
S
Sbjct: 74 HSS 76
>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 = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAF------VEYSRLEDAAEALKNI 153
L+V G+ + ++E++ + F ++G I++ D T + VEY ++A A++ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 154 NGRQIGGEQLRVDF 167
NG+ + G+ + VD+
Sbjct: 85 NGQDLMGQPISVDW 98
Score = 37.7 bits (86), Expect = 0.029, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 23 LWVGNLSADTTDADLKELFGKFGA-------LDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
L+V + + T+ D+ + F ++G LD+ T Y + + V ++ ++A+AA +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL-KGYTLVEYETYKEAQAAMEG 83
Query: 76 LQGSDFRGNPIKIEF 90
L G D G PI +++
Sbjct: 84 LNGQDLMGQPISVDW 98
Score = 31.2 bits (69), Expect = 3.1, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 11/82 (13%)
Query: 211 SVGRNRDGP-PSKIL--WVGYPPSVQMD--EQMLHNAMILFGEIERI------KSYPSRN 259
SV ++ D P P + + W+ + V + E+ +H+ +GEI+ I ++ +
Sbjct: 6 SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 65
Query: 260 YSFVEFRSVDEARRAKEGLQGR 281
Y+ VE+ + EA+ A EGL G+
Sbjct: 66 YTLVEYETYKEAQAAMEGLNGQ 87
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 22 NLWVGNLSADTTDADLKELFGKFGALDKVTTY-----SSRSFAFVYFKRVEDAKAAKDAL 76
L+VG L+ ++ D+ LF FG +D+ T SS+ AFV F +A+AA AL
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 77 QGS 79
GS
Sbjct: 77 HGS 79
Score = 31.6 bits (70), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 5/65 (7%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLK--DGNT---AFVEYSRLEDAAEALKN 152
+ L+VG +++ S+E++ F FG I++ L+ DG++ AFV++S +A A+
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 153 INGRQ 157
++G Q
Sbjct: 76 LHGSQ 80
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 6/65 (9%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALKN 152
+L+V G+ +T+S++E+E+ F ++G I + L D T F+ + + +A EA+K
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 153 INGRQ 157
+NG++
Sbjct: 63 LNGQK 67
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 10/80 (12%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFG-------ALDKVTTYSSRSFAFVYFKRVEDAKAAK 73
+NL+V L + ++++LF ++G LD+ T SR F+ F + +A+ A
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGV-SRGVGFIRFDKRIEAEEAI 60
Query: 74 DALQGSDFRG--NPIKIEFA 91
L G G PI ++FA
Sbjct: 61 KGLNGQKPLGAAEPITVKFA 80
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKN 152
+L++ + Q ++L + F+ FGN+ K D T FV Y A A+++
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 153 INGRQIGGEQLRVDFLRSQPSRREQWPNSHDARDGP 188
+NG QIG ++L+V RS+ +D++ GP
Sbjct: 87 MNGFQIGMKRLKVQLKRSK----------NDSKSGP 112
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 8/95 (8%)
Query: 11 AYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGA-------LDKVTTYSSRSFAFVYF 63
A KE P +NL++ +L + D DL ++F FG +DK T S+ F FV +
Sbjct: 16 AGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNL-SKCFGFVSY 74
Query: 64 KRVEDAKAAKDALQGSDFRGNPIKIEFARPAKPSK 98
A+AA ++ G +K++ R SK
Sbjct: 75 DNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 109
>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 = 40.0 bits (92), Expect = 0.006, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAF------VEYSRLEDAAEALKNI 153
L+V G+ + ++E++ + F ++G I++ D T + VEY ++A A++ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 154 NGRQIGGEQLRVDF 167
NG+ + G+ + VD+
Sbjct: 72 NGQDLMGQPISVDW 85
Score = 37.7 bits (86), Expect = 0.035, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 8/75 (10%)
Query: 23 LWVGNLSADTTDADLKELFGKFGA-------LDKVTTYSSRSFAFVYFKRVEDAKAAKDA 75
L+V + + T+ D+ + F ++G LD+ T Y + + V ++ ++A+AA +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL-KGYTLVEYETYKEAQAAMEG 70
Query: 76 LQGSDFRGNPIKIEF 90
L G D G PI +++
Sbjct: 71 LNGQDLMGQPISVDW 85
Score = 30.4 bits (67), Expect = 4.8, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 225 WVGYPPSVQMD--EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKE 276
W+ + V + E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A E
Sbjct: 10 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 69
Query: 277 GLQGR 281
GL G+
Sbjct: 70 GLNGQ 74
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 29/85 (34%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAKAA 72
++NL V L D TD +L LF G + D T YS +AFV F D++ A
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSY-GYAFVDFTSEMDSQRA 61
Query: 73 KDALQGSDFRGNPIKIEFARPAKPS 97
L G R +K+ +ARP S
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGES 86
Score = 33.1 bits (74), Expect = 0.85, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKN 152
+L V + Q ++ EL F G I + ++D T AFV+++ D+ A+K
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 153 INGRQIGGEQLRVDFLR 169
+NG + ++L+V + R
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 39.7 bits (91), Expect = 0.008, Method: Composition-based stats.
Identities = 28/71 (39%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSR-----SFAFVYFKRVEDAKAAKDALQ 77
++VGNL A + L ELF + G L KVT R SF FV FK E A L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 78 GSDFRGNPIKI 88
G G PI +
Sbjct: 79 GIRLYGRPINV 89
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 61
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A + QG F P +I++A+
Sbjct: 62 ATNALRSXQGFPFYDKPXRIQYAK 85
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 63
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A + QG F P +I++A+
Sbjct: 64 ATNALRSXQGFPFYDKPXRIQYAK 87
>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 = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKE----LFGKFG-ALDKVTTYS--SRSFAFVYFKRVED 68
E P+ +++ NL+ +LK+ +F +FG LD + + S R AFV FK V
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 64
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A + QG F P +I++A+
Sbjct: 65 ATNALRSXQGFPFYDKPXRIQYAK 88
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 39.7 bits (91), Expect = 0.009, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 45/79 (56%), Gaps = 6/79 (7%)
Query: 16 EAPPSSNLWVGNLSADTTDADLK----ELFGKFG-ALDKVTTYSSRSFAFVYFKRVEDAK 70
E+ NL++GNL+ + + A+LK ELF K A+ V T ++R F +V F+ ED +
Sbjct: 13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 72
Query: 71 AAKDALQGSDFRGNPIKIE 89
A + L G GN IK+E
Sbjct: 73 KALE-LTGLKVFGNEIKLE 90
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 39.7 bits (91), Expect = 0.009, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 18 PPSSN--LWVGNLSADTTDADLKELFGKFGALDKV---TTYSSRSFAFVYFKRVEDAKAA 72
PP N L++ NL T ++ ++FGK+G + ++ T +R A+V ++ + DAK A
Sbjct: 8 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 67
Query: 73 KDALQG 78
D L G
Sbjct: 68 CDHLSG 73
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 39.3 bits (90), Expect = 0.011, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDG-NTAFVEYSRLEDAAEALKNINGRQI 158
++VG + +K ELE F +G + ++ AFVE+ DAA+A+++++GR +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTL 135
Query: 159 GGEQLRVDF 167
G ++RV+
Sbjct: 136 CGCRVRVEL 144
Score = 37.4 bits (85), Expect = 0.039, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 18 PPSSNLWVGNLSADTTDADLKELFGKFGALDKV-TTYSSRSFAFVYFKRVEDAKAAKDAL 76
P ++VGNL + +L+ FG +G L V + FAFV F+ DA A L
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDL 130
Query: 77 QGSDFRGNPIKIEFARPAK 95
G G +++E + K
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 4/74 (5%)
Query: 22 NLWVGNLSADTTDADLKELFGKFG---ALDKVTTYSSRS-FAFVYFKRVEDAKAAKDALQ 77
L+VGNLS D T+ + +LF + G + +T ++S + FV F DA AA A+
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 78 GSDFRGNPIKIEFA 91
G G +K+ +A
Sbjct: 77 GRKILGKEVKVNWA 90
Score = 37.0 bits (84), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 52/88 (59%), Gaps = 5/88 (5%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT----AFVEYSRLEDAAEALKNI 153
+ L+VG +S+ V++ + + F + G + K + + + FVE+ DAA AL +
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 154 NGRQIGGEQLRVDFLRSQPSRREQWPNS 181
NGR+I G++++V++ + PS ++ P+S
Sbjct: 76 NGRKILGKEVKVNW-ATTPSSQKSGPSS 102
>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 = 38.9 bits (89), Expect = 0.013, Method: Composition-based stats.
Identities = 31/92 (33%), Positives = 48/92 (52%), Gaps = 7/92 (7%)
Query: 81 FRGNPIKIEFARPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKF-LKDGNTA--- 136
FRG+ + E + K S L+VG +S ++E++ E F K G+I+ L TA
Sbjct: 4 FRGDNEEQE--KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF 61
Query: 137 -FVEYSRLEDAAEALKNINGRQIGGEQLRVDF 167
FVEY DA A++ ING ++ +R D+
Sbjct: 62 CFVEYYSRADAENAMRYINGTRLDDRIIRTDW 93
Score = 35.4 bits (80), Expect = 0.16, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 9/78 (11%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFG-------ALDKVTTYSSRSFAFVYFKRVEDAKAA 72
S L+VGNLS TT+ + ELF K G LDK+ T + F FV + DA+ A
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT--ACGFCFVEYYSRADAENA 75
Query: 73 KDALQGSDFRGNPIKIEF 90
+ G+ I+ ++
Sbjct: 76 MRYINGTRLDDRIIRTDW 93
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 38.9 bits (89), Expect = 0.014, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAF------VEYSRLEDAAEALKNI 153
L+V I + ++E++E F +G I++ D T F VEY + A A + +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 154 NGRQIGGEQLRVDFLRSQPSRR 175
NG +I G+ ++VD+ + +R
Sbjct: 89 NGAEIMGQTIQVDWCFVKGPKR 110
>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 = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGAL-------DKVTTYSSRSFAFVYFKRVEDAKAAK 73
+NL V L + T +L+ LF G + DKV +S + FV + +DA+ A
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHS-LGYGFVNYVTAKDAERAI 78
Query: 74 DALQGSDFRGNPIKIEFARPA 94
+ L G + IK+ +ARP+
Sbjct: 79 NTLNGLRLQSKTIKVSYARPS 99
Score = 35.8 bits (81), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKD---GNT---AFVEYSRLEDAAEALKN 152
+L V + Q +++EL F G +E K ++D G++ FV Y +DA A+
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 153 INGRQIGGEQLRVDFLR 169
+NG ++ + ++V + R
Sbjct: 81 LNGLRLQSKTIKVSYAR 97
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.5 bits (88), Expect = 0.016, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDG-NTAFVEYSRLEDAAEALKNINGRQI 158
++VG + +K ELE F +G + ++ AFVE+ DAA+A++ ++GR +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 135
Query: 159 GGEQLRVDF 167
G ++RV+
Sbjct: 136 CGCRVRVEL 144
Score = 37.7 bits (86), Expect = 0.030, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 18 PPSSNLWVGNLSADTTDADLKELFGKFGALDKV-TTYSSRSFAFVYFKRVEDAKAAKDAL 76
P ++VGNL + +L+ FG +G L V + FAFV F+ DA A L
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVREL 130
Query: 77 QGSDFRGNPIKIEFARPAK 95
G G +++E + K
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 38.5 bits (88), Expect = 0.016, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 18 PPSSN--LWVGNLSADTTDADLKELFGKFGALDKV---TTYSSRSFAFVYFKRVEDAKAA 72
PP N L++ NL T ++ ++FGK+G + ++ T +R A+V ++ + DAK A
Sbjct: 14 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 73
Query: 73 KDALQG 78
D L G
Sbjct: 74 CDHLSG 79
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 38.5 bits (88), Expect = 0.017, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDG-NTAFVEYSRLEDAAEALKNINGRQI 158
++VG + K ELE F +G + ++ AFVE+ DA +A++ ++G+ I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 159 GGEQLRVDFLRSQPSR 174
G ++RV+ P R
Sbjct: 63 CGSRVRVELSTGMPRR 78
Score = 33.1 bits (74), Expect = 0.82, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKV-TTYSSRSFAFVYFKRVEDAKAAKDALQGSDF 81
++VGNL +L+ F +G L V + FAFV F+ DA+ A L G
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 82 RGNPIKIEFA 91
G+ +++E +
Sbjct: 63 CGSRVRVELS 72
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 38.5 bits (88), Expect = 0.019, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 18 PPSSN--LWVGNLSADTTDADLKELFGKFGALDKV---TTYSSRSFAFVYFKRVEDAKAA 72
PP N L++ NL T ++ ++FGK+G + ++ T +R A+V ++ + DAK A
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 63
Query: 73 KDALQG 78
D L G
Sbjct: 64 VDHLSG 69
>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 = 38.5 bits (88), Expect = 0.019, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAF------VEYSRLEDAAEALKNI 153
L+V I + ++E++E F +G I++ D T F VEY + A A + +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 154 NGRQIGGEQLRVDFLRSQPSRR 175
NG +I G+ ++VD+ + +R
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKR 156
Score = 30.4 bits (67), Expect = 4.4, Method: Composition-based stats.
Identities = 27/104 (25%), Positives = 46/104 (44%), Gaps = 16/104 (15%)
Query: 192 RGTGFSDNHSAYKRSHPQSSVGRNRD------GPPSKIL-WVGYPPSV--QMDEQMLHNA 242
+G GF + + + H V RN D GP + W+ + S+ + E +
Sbjct: 34 KGRGFGSDSNTREAIHSYERV-RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEK 92
Query: 243 MILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQG 280
+GEI+ I ++ S+ Y+ VE+ + +A AKE L G
Sbjct: 93 FCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG 136
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 38.1 bits (87), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALKN 152
+L++ + Q + +L FL FGN+ K D T+ FV + + A A+K
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 153 INGRQIGGEQLRV 165
+NG Q+G ++L+V
Sbjct: 102 MNGFQVGTKRLKV 114
Score = 37.0 bits (84), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 16 EAPPSSNLWVGNLSADTTDADLKELFGKFG-------ALDKVTTYSSRSFAFVYFKRVED 68
E P NL++ +L + TD DL F FG +DK T+ S+ F FV F +
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSL-SKCFGFVSFDNPDS 94
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A+ A A+ G +K++ +
Sbjct: 95 AQVAIKAMNGFQVGTKRLKVQLKK 118
>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 = 38.1 bits (87), Expect = 0.026, Method: Composition-based stats.
Identities = 25/65 (38%), Positives = 33/65 (50%), Gaps = 9/65 (13%)
Query: 24 WVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFKRVEDAKAAKDALQ 77
+VG LS DT+ DLK+ F KFG + T T SR F F+ FK DA + + L
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK---DAASVEKVLD 71
Query: 78 GSDFR 82
+ R
Sbjct: 72 QKEHR 76
Score = 31.6 bits (70), Expect = 2.1, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 101 WVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA 136
+VGG+S SK++L++ F KFG + D D NT
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTG 50
>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 = 0.026, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDA-AEALKNINGRQI 158
L+VGG+ T+++ +L F +FG I ++ AF++++ + A A K+ N +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIV 74
Query: 159 GGEQLRVDFLR 169
G +L V + R
Sbjct: 75 NGRRLNVKWGR 85
Score = 34.3 bits (77), Expect = 0.36, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 28/54 (51%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKD 74
+ L+VG L T+ DL+ F +FG + +T + AF+ F + A+ A +
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAE 66
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 37.7 bits (86), Expect = 0.033, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNINGRQ 157
K L+V ++ TV++E LE+ F +FG +E K LKD AFV + A +A+ +NG++
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--YAFVHFEDRGAAVKAMDEMNGKE 73
Query: 158 IGGEQLRVDFLRSQPSRREQWPNS 181
+ L P ++ P+S
Sbjct: 74 -IEGEEIEIVLAKPPDKKRSGPSS 96
Score = 32.0 bits (71), Expect = 1.6, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQGSDFR 82
L+V NL+ T+ L++ F +FG L++V + +AFV+F+ A A D + G +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEDRGAAVKAMDEMNGKEIE 75
Query: 83 GNPIKIEFARP 93
G I+I A+P
Sbjct: 76 GEEIEIVLAKP 86
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 37.7 bits (86), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 45/179 (25%), Positives = 68/179 (37%), Gaps = 24/179 (13%)
Query: 18 PPSSNLWVGNLSADTTDADLKELFGKFGALDKV-TTYSSRS-----FAFVYFKRVEDAKA 71
P + L V NL T +EL FG+L++ YS R+ + F + + + A
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
Query: 72 AKDALQGSDFRGNPIKIEFARPAKPSKHLWVGGISQTVSKEELEEGF---------LKFG 122
AK L G + + + + + L S+ + + L GF L
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALL---HSRCLCVDRLPPGFNDVDALCRALSAV 209
Query: 123 NIEDFKFLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRVDFLRSQPSRR 175
+ F L G A +EY E A EA + +G +GG LRV F P R
Sbjct: 210 HSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGR 268
Score = 30.8 bits (68), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 219 PPSKILWVG-YPPSVQMDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEA 271
P +L V PPS + +Q + FG +ER ++ S+ Y F E+ D A
Sbjct: 93 PTDALLCVANLPPS--LTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150
Query: 272 RRAKEGLQGR 281
RAK L G+
Sbjct: 151 ARAKSDLLGK 160
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 37.4 bits (85), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 66/172 (38%), Gaps = 24/172 (13%)
Query: 18 PPSSNLWVGNLSADTTDADLKELFGKFGALDKV-TTYSSRS-----FAFVYFKRVEDAKA 71
P + L V NL T +EL FG+L++ YS R+ + F + + + A
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
Query: 72 AKDALQGSDFRGNPIKIEFARPAKPSKHLWVGGISQTVSKEELEEGF---------LKFG 122
AK L G + + + + + L S+ + + L GF L
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALL---HSRCLCVDRLPPGFNDVDALCRALSAV 209
Query: 123 NIEDFKFLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRVDFL 168
+ F L G A +EY E A EA + +G +GG LRV F
Sbjct: 210 HSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 219 PPSKILWVG-YPPSVQMDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEA 271
P +L V PPS + +Q + FG +ER ++ S+ Y F E+ D A
Sbjct: 93 PTDALLCVANLPPS--LTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150
Query: 272 RRAKEGLQGR 281
RAK L G+
Sbjct: 151 ARAKSDLLGK 160
>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 = 37.4 bits (85), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 45/179 (25%), Positives = 68/179 (37%), Gaps = 24/179 (13%)
Query: 18 PPSSNLWVGNLSADTTDADLKELFGKFGALDKV-TTYSSRS-----FAFVYFKRVEDAKA 71
P + L V NL T +EL FG+L++ YS R+ + F + + + A
Sbjct: 91 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 150
Query: 72 AKDALQGSDFRGNPIKIEFARPAKPSKHLWVGGISQTVSKEELEEGF---------LKFG 122
AK L G + + + + + L S+ + + L GF L
Sbjct: 151 AKSDLLGKPLGPRTLYVHWTDAGQLTPALL---HSRCLCVDRLPPGFNDVDALCRALSAV 207
Query: 123 NIEDFKFLKDGNT------AFVEYSRLEDAAEALKNINGRQIGGEQLRVDFLRSQPSRR 175
+ F L G A +EY E A EA + +G +GG LRV F P R
Sbjct: 208 HSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGR 266
Score = 30.8 bits (68), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 219 PPSKILWVG-YPPSVQMDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEA 271
P +L V PPS + +Q + FG +ER ++ S+ Y F E+ D A
Sbjct: 91 PTDALLCVANLPPS--LTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 148
Query: 272 RRAKEGLQGR 281
RAK L G+
Sbjct: 149 ARAKSDLLGK 158
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 37.4 bits (85), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAAKDAL 76
L+V NLS +++ DL++LF +G L ++ T + FAFV F E A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 77 QGSDFRGNPIKI 88
G F+G + +
Sbjct: 71 DGQVFQGRMLHV 82
>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 = 37.4 bits (85), Expect = 0.042, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAK 70
++VG LS DT + ++E FG FG ++ + T R F F+ FK E K
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 57
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.4 bits (85), Expect = 0.043, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAK 70
++VG LS DT + ++E FG FG ++ + T R F F+ FK E K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 55
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 37.4 bits (85), Expect = 0.045, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 18 PPSSN--LWVGNLSADTTDADLKELFGKFGALDKV---TTYSSRSFAFVYFKRVEDAKAA 72
PP N L + NL T ++ ++FGK+G + ++ T +R A+V ++ + DAK A
Sbjct: 14 PPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 73
Query: 73 KDALQG 78
D L G
Sbjct: 74 CDHLSG 79
>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 = 37.0 bits (84), Expect = 0.046, Method: Composition-based stats.
Identities = 31/93 (33%), Positives = 48/93 (51%), Gaps = 8/93 (8%)
Query: 81 FRGNPIKIEFARPAKPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDG--NTA-- 136
FRG+ + E + K S L+VG +S ++E++ E F K G+I+ D TA
Sbjct: 25 FRGDNEEQE--KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 137 --FVEYSRLEDAAEALKNINGRQIGGEQLRVDF 167
FVEY DA A++ ING ++ +R D+
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDW 115
Score = 33.9 bits (76), Expect = 0.40, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFKRVEDAKAAK 73
S L+VGNLS TT+ + ELF K G + K+ ++ F FV + DA+ A
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 74 DALQGSDFRGNPIKIEF 90
+ G+ I+ ++
Sbjct: 99 RYINGTRLDDRIIRTDW 115
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.0 bits (84), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 5/87 (5%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA----FVEYSRLEDAAEALKNIN 154
+L+V + + E L + F FG I K + +G + FV +S E+A +A+ +N
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 155 GRQIGGEQLRVDFLRSQPSRREQWPNS 181
GR + + L V L + R+ P+S
Sbjct: 77 GRIVATKPLYVA-LAQRKEERQSGPSS 102
Score = 33.5 bits (75), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 22 NLWVGNLSADTTDADLKELFGKFGALD--KVTTYSSRS--FAFVYFKRVEDAKAAKDALQ 77
NL+V NL D L++ F FG + KV RS F FV F E+A A +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 78 GSDFRGNPIKIEFAR 92
G P+ + A+
Sbjct: 77 GRIVATKPLYVALAQ 91
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.0 bits (84), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 224 LWVGYPPSVQMDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEG 277
L V Y P+ +DE L +G IE +K + SR Y FV+F+S A++A G
Sbjct: 45 LMVNYIPTT-VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 278 LQGRLFNDPRITIMFSSS 295
L G + R+ + ++S
Sbjct: 104 LNGFNILNKRLKVALAAS 121
Score = 36.6 bits (83), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALK 151
++L V I TV + +L + F ++G IE K + D T FV++ A +A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 152 NINGRQIGGEQLRVDFLRSQPSR 174
+NG I ++L+V S R
Sbjct: 103 GLNGFNILNKRLKVALAASGHQR 125
Score = 35.8 bits (81), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 11/94 (11%)
Query: 4 PPSKFNRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRS 57
PP++ N E NL V + + L++LF ++G ++ V T SR
Sbjct: 31 PPTQMN-----PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 85
Query: 58 FAFVYFKRVEDAKAAKDALQGSDFRGNPIKIEFA 91
+ FV F+ A+ A L G + +K+ A
Sbjct: 86 YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119
>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 = 37.0 bits (84), Expect = 0.057, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 98 KH-LWVGGISQTVSKEELEEGFLKFGNIEDFKFL-----KDGNTAFVEYSRLEDAAEALK 151
KH L++ G+ + +KEELEE G ++D + + K A+VEY A++A+
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 152 NINGRQIGGEQLRVDFLRSQPS 173
++G I ++V S PS
Sbjct: 77 KMDGMTIKENIIKVAISNSGPS 98
>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 = 37.0 bits (84), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 99 HLWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTA------FVEYSRLEDAAEALKN 152
H++VG +S ++ + F FG I D + +KD T FV + DA A++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 153 INGRQIGGEQLRVDFLRSQP 172
+ G+ +GG Q+R ++ +P
Sbjct: 68 MGGQWLGGRQIRTNWATRKP 87
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 36.6 bits (83), Expect = 0.068, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 17 APPSSNLWVGNLSADTTDADLKELFGKFGALD-KVTTYSSRSFAFVYFKRVEDAKAAKDA 75
AP +++++VGNL D +DLK + G++ ++T R AF+++ A+ A
Sbjct: 16 APLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSC 75
Query: 76 LQGSDFRGNPIKIEFARPAK 95
LQG + +++ AR +
Sbjct: 76 LQGLRLGTDTLRVALARQQR 95
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 36.2 bits (82), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKV-------TTYSSRSFAFVYFKRVEDAKAA 72
SS +++GNL + + L + F FG + + T +S+ +AF+ F + + AA
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 73 KDALQGSDFRGNPIKIEFA 91
+A+ G PI + +A
Sbjct: 65 IEAMNGQYLCNRPITVSYA 83
Score = 34.3 bits (77), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 233 QMDEQMLHNAMILFGEI---ERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFND 285
++DE++L++ FG I +I P S+ Y+F+ F S D + A E + G+ +
Sbjct: 16 EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCN 75
Query: 286 PRITIMFS 293
IT+ ++
Sbjct: 76 RPITVSYA 83
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 36.2 bits (82), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 7/77 (9%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFG-ALDKVTTYSSRSFAFVYFKRVEDAKAAKDALQG 78
SS ++VG + D T+ +L+E F ++G +D R+FAFV F + A+ +L G
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQ----SLCG 60
Query: 79 SDF--RGNPIKIEFARP 93
D +G + I A P
Sbjct: 61 EDLIIKGISVHISNAEP 77
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYF 63
+++G LS TT L+E FG+FG + + T SR F FV F
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 6/83 (7%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKFGALD------KVTTYSSRSFAFVYFKRVEDAKAA 72
P+ L++ NLS T+ DL LF +F ++ T R AF+ F E A A
Sbjct: 24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 83
Query: 73 KDALQGSDFRGNPIKIEFARPAK 95
+ G G + IEF + K
Sbjct: 84 LHLVNGYKLYGKILVIEFGKNKK 106
Score = 33.5 bits (75), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 47/88 (53%), Gaps = 6/88 (6%)
Query: 93 PAKPSKHLWVGGISQTVSKEELEEGFLKF----GNIEDFKFL--KDGNTAFVEYSRLEDA 146
P +P+K L++ +S V++ +L F +F G F+ + + AF+ + E A
Sbjct: 21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 80
Query: 147 AEALKNINGRQIGGEQLRVDFLRSQPSR 174
+AL +NG ++ G+ L ++F +++ R
Sbjct: 81 WQALHLVNGYKLYGKILVIEFGKNKKQR 108
>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 = 35.8 bits (81), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFL------KDGNTAFVEYSRLEDAAEALK 151
K L+V ++ ++ +L F +G I+ + K AF+EY D A K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 152 NINGRQIGGEQLRVDFLRSQ 171
+ +G++I G ++ VD R +
Sbjct: 163 HADGKKIDGRRVLVDVERGR 182
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 3/92 (3%)
Query: 4 PPSKFNRAYDD--KEAPPS-SNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAF 60
PP +A D + APP + ++GN+ T+ADL LF FG + Y + F
Sbjct: 8 PPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCF 67
Query: 61 VYFKRVEDAKAAKDALQGSDFRGNPIKIEFAR 92
+ + E A AL F+G ++ + +
Sbjct: 68 IKYDTHEQAAVCIVALANFPFQGRNLRTGWGK 99
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.4 bits (80), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKVT-------TYSSRSFAFVYFKRVEDAKAA 72
+S + V N+ +++ELF FG L V T + R F FV F +DAK A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 73 KDAL-QGSDFRGNPIKIEFA 91
+AL + G + +E+A
Sbjct: 75 FNALCHSTHLYGRRLVLEWA 94
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 35.4 bits (80), Expect = 0.16, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 6/48 (12%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYFK 64
++VG LS +TT D+K F +FG +D TT R F FV F+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFE 49
>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 = 35.4 bits (80), Expect = 0.17, Method: Composition-based stats.
Identities = 29/93 (31%), Positives = 43/93 (46%), Gaps = 11/93 (11%)
Query: 234 MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 289
+D + L++ FG I K S+ Y FV F + + A RA E + G L ND ++
Sbjct: 17 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 76
Query: 290 I-MFSS-----SEL-APGKDYPGSYSGTKGPRS 315
+ F S +EL A K++ Y GP S
Sbjct: 77 VGRFKSRKEREAELGARAKEFTNVYIKNFGPGS 109
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 100 LWVGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNT------AFVEYSRLEDAAEALKNI 153
++VGG+ + VS+ L E FL+ G + + KD T FVE+ EDA A+K +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 154 NGRQIGGEQLRVD 166
+ ++ G+ +RV+
Sbjct: 78 DMIKLYGKPIRVN 90
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 16 EAPPSSNLWVGNLSADTTDA----DLKELFGKFG-ALDKVT--TYSSRSFAFVYFKRVED 68
E P+ +++ NL+ L +F +FG LD V T R AFV FK +
Sbjct: 2 EMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGS 61
Query: 69 AKAAKDALQGSDFRGNPIKIEFAR 92
A A +QG F P++I +++
Sbjct: 62 ASNALRTMQGFPFYDKPMQIAYSK 85
>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 = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 98 KHLWVGGISQTVSKEELEEGFLKFGNIEDFKFL------KDGNTAFVEYSRLEDAAEALK 151
K L+V ++ ++ +L F +G I+ + K AF+EY D A K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 152 NINGRQIGGEQLRVDFLRSQ 171
+ +G++I G ++ VD R +
Sbjct: 163 HADGKKIDGRRVLVDVERGR 182
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 34.7 bits (78), Expect = 0.23, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 234 MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 289
+D + L++ FG I K S+ Y FV F + + A RA E + G L ND ++
Sbjct: 23 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 82
Query: 290 I 290
+
Sbjct: 83 V 83
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 34.7 bits (78), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 5/88 (5%)
Query: 14 DKEAPPSSN--LWVGNL-SADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAK 70
+K P S N +++GNL +A +D++ +F K+G + + + + +AFV + A+
Sbjct: 19 NKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--KGYAFVQYSNERHAR 76
Query: 71 AAKDALQGSDFRGNPIKIEFARPAKPSK 98
AA G G + I A KP +
Sbjct: 77 AAVLGENGRVLAGQTLDINMAGEPKPDR 104
Score = 33.1 bits (74), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 93 PAKPSKHLWVGGISQT-VSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALK 151
P + +++G ++ V K ++E F K+G + K AFV+YS A A+
Sbjct: 23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--GYAFVQYSNERHARAAVL 80
Query: 152 NINGRQIGGEQLRVDF 167
NGR + G+ L ++
Sbjct: 81 GENGRVLAGQTLDINM 96
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 34.7 bits (78), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKFGA-----LDKVTTYSSRSF--AFVYFKRVEDAKA 71
PS + + N++ + L+ L + LD V S + A++ F E A+A
Sbjct: 28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQA 87
Query: 72 AKDALQGSDFRGNPIKIEFAR 92
+A QG F+GNP+ I F+
Sbjct: 88 FVEAFQGYPFQGNPLVITFSE 108
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 34.3 bits (77), Expect = 0.37, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 45/77 (58%), Gaps = 10/77 (12%)
Query: 95 KPSKHLWVGGISQTVSKEELEEGFLKFGNIEDFKF--------LKDGNTAFVEYSRLEDA 146
KP+K + +G +++ V+K+ + E F +G I+ L G A+VE+ ++A
Sbjct: 3 KPTK-VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG-YAYVEFENPDEA 60
Query: 147 AEALKNINGRQIGGEQL 163
+ALK+++G QI G+++
Sbjct: 61 EKALKHMDGGQIDGQEI 77
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 249 IERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP 299
+ER+ + S+ Y++VEF + DEA +A + + G + IT +++ LAP
Sbjct: 38 VERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT---ATAVLAP 85
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 34.3 bits (77), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 4/90 (4%)
Query: 93 PAKPSKHLWVGGISQ-TVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALK 151
P + +++G ++ V K ++E F K+G I K AFV+Y +A A+
Sbjct: 11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--GFAFVQYVNERNARAAVA 68
Query: 152 NINGRQIGGEQLRVDFLRSQPSRREQWPNS 181
+GR I G+ L ++ L ++P P+S
Sbjct: 69 GEDGRMIAGQVLDIN-LAAEPKVNRSGPSS 97
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 33.9 bits (76), Expect = 0.43, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 23 LWVGNLSADTTDADLKELFGKFGALDKV------TTYSSRSFAFVYF 63
+++G LS TT L+E FG+FG + + T SR F FV F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>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 = 33.9 bits (76), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 18 PPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTY--SSRSFAFVYFKRVEDAKAAKDA 75
PPS+ L + N+ ++ DLK LF G + K + R A + VE+A A
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 208
Query: 76 LQGSDFRGN-PIKIEFAR 92
L D N +++ F++
Sbjct: 209 LHNHDLGENHHLRVSFSK 226
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 33.5 bits (75), Expect = 0.59, Method: Composition-based stats.
Identities = 17/33 (51%), Positives = 19/33 (57%)
Query: 59 AFVYFKRVEDAKAAKDALQGSDFRGNPIKIEFA 91
A V F AKAA D G +F GNPIK+ FA
Sbjct: 66 ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 33.5 bits (75), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 18 PPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTY--SSRSFAFVYFKRVEDAKAAKDA 75
PPS+ L + N+ ++ DLK LF G + K + R A + VE+A A
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 177
Query: 76 LQGSDFRGN-PIKIEFAR 92
L D N +++ F++
Sbjct: 178 LHNHDLGENHHLRVSFSK 195
>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 = 33.1 bits (74), Expect = 0.69, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSS------RSFAFVYFKRVEDAKAAK 73
+ +++VGN+ T +L+ F G++++VT + FA++ F E + +
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 74 DALQGSDFRGNPIKIEFARPAKP 96
AL S FRG IK+ R +P
Sbjct: 65 -ALDESLFRGRQIKVIPKRTNRP 86
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 33.1 bits (74), Expect = 0.71, Method: Composition-based stats.
Identities = 17/33 (51%), Positives = 19/33 (57%)
Query: 59 AFVYFKRVEDAKAAKDALQGSDFRGNPIKIEFA 91
A V F AKAA D G +F GNPIK+ FA
Sbjct: 60 ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 32.7 bits (73), Expect = 0.89, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 20 SSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSS------RSFAFVYFKRVEDAKAAK 73
+ +++VGN+ T +L+ F G++++VT + FA++ F E + +
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 74 DALQGSDFRGNPIKIEFARPAKP 96
AL S FRG IK+ R +P
Sbjct: 66 -ALDESLFRGRQIKVIPKRTNRP 87
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 37/95 (38%), Gaps = 7/95 (7%)
Query: 197 SDNHSAYKRSHPQSSVGRNRDGPPSKILWVGYPPSVQMDEQMLHNAMILFGE-----IER 251
S S K S Q+ + + ++ P+ + P + MDEQ L N + FG+ I R
Sbjct: 2 SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLP--LSMDEQELENMLKPFGQVISTRILR 59
Query: 252 IKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDP 286
S SR F S ++ G+ P
Sbjct: 60 DSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP 94
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 7/82 (8%)
Query: 19 PSSNLWVGNLSADTTDADLKELFGKF------GALDKVTTYSSRSFAFVYFKRVEDAKAA 72
P +L+VG+L+ D D L E F K G + T S+ + FV F + K A
Sbjct: 8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRA 67
Query: 73 KDALQGSDFRGN-PIKIEFARP 93
QG+ G+ P+++ A P
Sbjct: 68 LTECQGAVGLGSKPVRLSVAIP 89
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 28/111 (25%), Positives = 50/111 (45%), Gaps = 16/111 (14%)
Query: 4 PPSKFNRAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSS------RS 57
PP + ++K+ +++VGN+ +T DL+ F G+++++T +
Sbjct: 22 PPQPL--SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG 79
Query: 58 FAFVYFKRVEDAKAAKDALQGSDFRGNPIKIEFARPAKPSKHLWVGGISQT 108
+A++ F AA A+ + FRG IK+ R P GIS T
Sbjct: 80 YAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMP-------GISST 122
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 13/100 (13%)
Query: 10 RAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTY-----------SSRSF 58
R+Y+ E P+ ++V NL+ + DLK +FG++ T +
Sbjct: 37 RSYEPGE--PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQ 94
Query: 59 AFVYFKRVEDAKAAKDALQGSDFRGNPIKIEFARPAKPSK 98
AF+ + A A G G P+ ++FAR A+P +
Sbjct: 95 AFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQ 134
>pdb|1MU2|B Chain B, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 426
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 850 QGTEASTLYGSSVFQQPNNPTAVSNQ-VNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLS 908
QG + S +Q P +N+ V + Q + + ++ D+ +LEH V QL+ +L+
Sbjct: 146 QGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDRTDLEHDRVVLQLKELLN 205
Query: 909 GAGQGTSDGEVDKNQRY 925
G G T D + K+ Y
Sbjct: 206 GLGFSTPDEKFQKDPPY 222
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 31.6 bits (70), Expect = 2.3, Method: Composition-based stats.
Identities = 37/174 (21%), Positives = 65/174 (37%), Gaps = 25/174 (14%)
Query: 23 LWVGNLSADTTDADLKELFGKFGA------LDKVTTYSSRSFAFVYFKRVEDAKAAKDAL 76
LW N T ++++L L + +SR FA++ EDA+ + L
Sbjct: 120 LWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179
Query: 77 QGSDFRGNPIKIEFARPAKPSKHLWVGGIS------QTVSKEELEEGFLK-----FGNIE 125
G G + + + P + SK + + +S E L+E L+ FG+IE
Sbjct: 180 NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIE 239
Query: 126 DFKFLK-------DGNTAFVEYSRLEDAAEALKNINGRQIGGEQLRVDFLRSQP 172
+ AF + + A AL+ N +G ++ V +P
Sbjct: 240 KINIPAGQKEHSFNNCCAFXVFENKDSAERALQX-NRSLLGNREISVSLADKKP 292
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 31.6 bits (70), Expect = 2.4, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 1/87 (1%)
Query: 10 RAYDDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTY-SSRSFAFVYFKRVED 68
+ D K+ + L NL T +LKE+F + V+ S+ A++ FK D
Sbjct: 83 KGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEAD 142
Query: 69 AKAAKDALQGSDFRGNPIKIEFARPAK 95
A+ + QG++ G I + + K
Sbjct: 143 AEKTFEEKQGTEIDGRSISLYYTGEPK 169
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 16/99 (16%)
Query: 13 DDKEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKR------- 65
D E +S ++V L+ T DL + F + G + K+ + + +Y +
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVV-KMNKRTGQPMIHIYLDKETGKPKG 66
Query: 66 -----VED---AKAAKDALQGSDFRGNPIKIEFARPAKP 96
ED AKAA + G DF+G+ +K+ AR P
Sbjct: 67 DATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 31.2 bits (69), Expect = 2.9, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 137 FVEYSRLEDAAEALKNINGRQIGGEQLRVDF 167
F+E+ R+E A +A+ ++NGR GG ++ F
Sbjct: 60 FLEFERVESAIKAVVDLNGRYFGGRVVKACF 90
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 31.2 bits (69), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 6/61 (9%)
Query: 18 PPSSNLWVGNL-SADTTDADLKELFGKFGALDKVTTYSSRSFAFVYFKRVEDAKAAKDAL 76
PP S L++GNL + + DL +F +G + ++ +F F+ F ++ ++ +DA+
Sbjct: 8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQF---DNPQSVRDAI 62
Query: 77 Q 77
+
Sbjct: 63 E 63
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVT------TYSSRSFAFVYFK-RVEDAKAAK 73
+ ++VG L TTDA L++ F FG +++ T SR + FV R +A K
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 74 D 74
D
Sbjct: 78 D 78
>pdb|1G6E|A Chain A, Antifungal Protein From Streptomyces Tendae Tu901, 30-
Conformers Ensemble
pdb|1GH5|A Chain A, Antifungal Protein From Streptomyces Tendae Tu901, Nmr
Average Structure
Length = 87
Score = 31.2 bits (69), Expect = 3.2, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 851 GTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSV 906
GT +YG + + NN + Q NLS P+ + T+++ K +P H+ ++ S+
Sbjct: 30 GTMPVAIYGVNWVESGNNVVTLQFQRNLSDPR-LETITLQKWGSWNPGHIHEILSI 84
>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 555
Score = 30.8 bits (68), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 850 QGTEASTLYGSSVFQQPNNPTAVSNQ-VNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLS 908
QG + S +Q P +N+ V + Q + + ++ D+ +LEH V QL+ +L+
Sbjct: 151 QGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDRTDLEHDRVVLQLKELLN 210
Query: 909 GAGQGTSDGEVDKNQRY 925
G G T D + K+ Y
Sbjct: 211 GLGFSTPDEKFQKDPPY 227
>pdb|1NHC|A Chain A, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|B Chain B, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|C Chain C, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|D Chain D, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|E Chain E, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|F Chain F, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
Length = 336
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 455 IDDHGLVLDQSYGLGSITGGPASG---AFVNVQG-RNRLSPVASKVTAGGFGRNPIDSDF 510
I D+G+V++Q Y GS TG P++G V V G L A++V + SD+
Sbjct: 254 ITDYGIVIEQDYENGSPTGTPSTGIPITDVTVDGVTGTLEDDATQVYI--LCGDGSCSDW 311
Query: 511 IWRGIIAKGGTPVCRARCVPFG 532
W G+ GG + VP G
Sbjct: 312 TWSGVDLSGGKTSDKCENVPSG 333
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 102 VGGISQTVSKEELEEGFLKFGNIEDFKFLKDGNTAFVEYSRLEDAAEALKNINGRQIGGE 161
V G+ + S ++L++ + G++ KDG VEY R ED AL+ ++ +
Sbjct: 20 VSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-MGMVEYLRKEDMEYALRKLDDTKFRSH 78
Query: 162 QLRVDFLRSQPSR 174
+ ++R P R
Sbjct: 79 EGETSYIRVYPER 91
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 30.4 bits (67), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 10/64 (15%)
Query: 221 SKILWVGYPPSVQMDEQML--HNAMILFGEIERIKSYP--------SRNYSFVEFRSVDE 270
++ L+VG P +E M+ NA + G + + P +N++F+EFRSVDE
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 271 ARRA 274
+A
Sbjct: 66 TTQA 69
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.4 bits (67), Expect = 5.3, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 15 KEAPPSSNLWVGNLSADTTDADLKELFGKFGALDKVTT-YSSRSFAFVYFKRVEDAKAAK 73
K+ + L NLS + T+ +LKE+F + V+ S+ A++ FK DA+
Sbjct: 11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNL 70
Query: 74 DALQGSDFRGNPIKIEF 90
+ QG++ G + + +
Sbjct: 71 EEKQGAEIDGRSVSLYY 87
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 10/64 (15%)
Query: 221 SKILWVGYPPSVQMDEQML--HNAMILFGEIERIKSYP--------SRNYSFVEFRSVDE 270
++ L+VG P +E M+ NA + G + + P +N++F+EFRSVDE
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60
Query: 271 ARRA 274
+A
Sbjct: 61 TTQA 64
>pdb|3R7K|A Chain A, Crystal Structure Of A Probable Acyl Coa Dehydrogenase
From Mycobacterium Abscessus Atcc 19977 DSM 44196
pdb|3R7K|B Chain B, Crystal Structure Of A Probable Acyl Coa Dehydrogenase
From Mycobacterium Abscessus Atcc 19977 DSM 44196
pdb|3R7K|C Chain C, Crystal Structure Of A Probable Acyl Coa Dehydrogenase
From Mycobacterium Abscessus Atcc 19977 DSM 44196
pdb|3R7K|D Chain D, Crystal Structure Of A Probable Acyl Coa Dehydrogenase
From Mycobacterium Abscessus Atcc 19977 DSM 44196
Length = 403
Score = 29.6 bits (65), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 53/128 (41%), Gaps = 15/128 (11%)
Query: 499 GGFGRNPIDSDFIWRGIIAKGG-TPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKH 557
GG G N IDS + I+A GG T VC A F GI LP + A G D L +
Sbjct: 84 GGSGGNAIDSALVTEAILAAGGSTGVCAA---LFTHGI--ALPHI----AANGSDALIER 134
Query: 558 YAE-AIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPP--SDFLS 614
Y + ++ L +E S LR R G +G F+ +DF++
Sbjct: 135 YVRPTLAGKMIGSLGVTEPGAGSDVANLRT--RAVREGDTYVVNGAKTFITSGVRADFVT 192
Query: 615 KVLKVVGP 622
++ GP
Sbjct: 193 TAVRTGGP 200
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 29.6 bits (65), Expect = 9.5, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 11/81 (13%)
Query: 21 SNLWVGNLSADTTDADLKELFGKFGALDKVTTY------SSRSFAFVYFKRVEDAKAAKD 74
+ ++VG + + + +L+E F KFG + +V R F F+ F ED ++
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF---EDEQSVDQ 67
Query: 75 A--LQGSDFRGNPIKIEFARP 93
A + D G ++++ A P
Sbjct: 68 AVNMHFHDIMGKKVEVKRAEP 88
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
0.314 0.132 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,886,318
Number of Sequences: 62578
Number of extensions: 1290546
Number of successful extensions: 2489
Number of sequences better than 100.0: 194
Number of HSP's better than 100.0 without gapping: 99
Number of HSP's successfully gapped in prelim test: 95
Number of HSP's that attempted gapping in prelim test: 2084
Number of HSP's gapped (non-prelim): 391
length of query: 957
length of database: 14,973,337
effective HSP length: 108
effective length of query: 849
effective length of database: 8,214,913
effective search space: 6974461137
effective search space used: 6974461137
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (26.2 bits)