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= 037453
(216 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 158 bits (400), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 78/129 (60%), Positives = 92/129 (71%)
Query: 42 KLSAYRDRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDK 101
+LS YRD+ F G EE E+ L S T+YVGN+SFYTTEEQIYELFS++G+IKKIIMGLDK
Sbjct: 16 ELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK 75
Query: 102 NSKTPCGFCFALFYSREDTEDAVKYISGTILDDRPIRVDFDWGFXXXXXXXXXXXXXXVR 161
KT CGFCF +YSR D E+A++YI+GT LDDR IR D+D GF VR
Sbjct: 76 MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVR 135
Query: 162 DEYRTDYDP 170
DEYR DYD
Sbjct: 136 DEYRQDYDA 144
>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 = 131 bits (329), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 65/98 (66%), Positives = 78/98 (79%), Gaps = 1/98 (1%)
Query: 48 DRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPC 107
D+ F G EE E+ L S T+YVGN+SFYTTEEQIYELFS++G+IKKIIMGLDK KT C
Sbjct: 1 DQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTAC 59
Query: 108 GFCFALFYSREDTEDAVKYISGTILDDRPIRVDFDWGF 145
GFCF +YSR D E+A++YI+GT LDDR IR D+D GF
Sbjct: 60 GFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGF 97
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 56.6 bits (135), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 48/73 (65%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
++VG +SF T E+ + ++FS+ G+I ++++ D+ ++ GF F F + +D +DA+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 128 SGTILDDRPIRVD 140
+G +D R IRVD
Sbjct: 75 NGKSVDGRQIRVD 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%)
Query: 72 NMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYISGTI 131
+S YTTE + E+FS+ G I + + D+ S+ GF F F + +D ++A + +G
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 132 LDDRPIRVDF 141
LD R IRVDF
Sbjct: 113 LDGRRIRVDF 122
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 41/69 (59%)
Query: 73 MSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYISGTIL 132
+S YTTE + E+FS+ G I + + D+ S+ GF F F + +D ++A + +G L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 133 DDRPIRVDF 141
D R IRVDF
Sbjct: 83 DGRRIRVDF 91
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 41/69 (59%)
Query: 73 MSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYISGTIL 132
+S YTTE + E+FS+ G I + + D+ S+ GF F F + +D ++A + +G L
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
Query: 133 DDRPIRVDF 141
D R IRVDF
Sbjct: 80 DGRRIRVDF 88
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 43/74 (58%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
T++ V N+++ T+ + + +F + G + + + D+ +K GF F F+ + D EDA+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 126 YISGTILDDRPIRV 139
+ G +LD R +RV
Sbjct: 131 AMDGAVLDGRELRV 144
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 43/74 (58%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
T++ V N+++ T+ + + +F + G + + + D+ +K GF F F+ + D EDA+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 126 YISGTILDDRPIRV 139
+ G +LD R +RV
Sbjct: 108 AMDGAVLDGRELRV 121
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 41/73 (56%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
T+ V N+++ T+ + + +F + G + + + + ++K P GF F F+ R D +DA
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 127 ISGTILDDRPIRV 139
+ G LD R +RV
Sbjct: 75 MDGAELDGRELRV 87
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 32/90 (35%), Positives = 44/90 (48%), Gaps = 8/90 (8%)
Query: 51 FPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFC 110
FP +E A TV+VGN+ EE +YELF +AG + K+ + D+ K P F
Sbjct: 9 FPAQEE-------ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFG 60
Query: 111 FALFYSREDTEDAVKYISGTILDDRPIRVD 140
F F E A+ ++G L RPI V
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGRPINVS 90
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 42/75 (56%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
+ +TVYV N+ F T +Y +FS+ G++ K+ + DK+++ G F LF ++ ++
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 124 VKYISGTILDDRPIR 138
+ I+ L R I+
Sbjct: 75 TRAINNKQLFGRVIK 89
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+V+VGN+ + TEEQ+ ++FS G + + D+ + P G+ F + +E A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 127 ISGTILDDRPIRVD 140
++G R +RVD
Sbjct: 70 LNGREFSGRALRVD 83
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 39/67 (58%)
Query: 73 MSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYISGTIL 132
+S YTTE + E+FS+ G I + + D+ S+ GF F F + +D ++A + +G L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 133 DDRPIRV 139
D R IRV
Sbjct: 83 DGRRIRV 89
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+YVGN+ + T EQ+ ELFS+ G++ + + D+ +K P GF F E +A+ +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 128 SGTILDDRPIRV 139
T R IRV
Sbjct: 63 DNTDFMGRTIRV 74
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 47.0 bits (110), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
TVYVG + +E ++ELF +AG + M D+ + G+ F F S ED + A+K
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 126 YISGTILDDRPIRVD 140
+ L +PIRV+
Sbjct: 76 IMDMIKLYGKPIRVN 90
>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 = 47.0 bits (110), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 40/81 (49%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
A T++V +++ TTE ++ F G IK+I M K S P G+ F + D A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 124 VKYISGTILDDRPIRVDFDWG 144
K+ G +D R + VD + G
Sbjct: 161 YKHADGKKIDGRRVLVDVERG 181
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
++VGN+ TEE LF R GE ++ + D+ GF F SR E A +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 128 SGTILDDRPIRVDF 141
GTIL RP+R+ F
Sbjct: 79 DGTILKSRPLRIRF 92
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 34/65 (52%)
Query: 65 STTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV 124
+ T+ V N+S T E + ELF G I +I + DK + GF F F+ RED A+
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Query: 125 KYISG 129
+SG
Sbjct: 75 AGVSG 79
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
T++V +++ TTE ++ F G IK+I M K S P G+ F + D A K+
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 127 ISGTILDDRPIRVDFDWG 144
G +D R + VD + G
Sbjct: 164 ADGKKIDGRRVLVDVERG 181
>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 = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 50/98 (51%), Gaps = 5/98 (5%)
Query: 44 SAYRDRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNS 103
S +D PG Q E +L T V+ TEE I++ F+ GEIK I + LD+ +
Sbjct: 6 SVEQDGDEPGPQRSVEGWILFVTGVHE-----EATEEDIHDKFAEYGEIKNIHLNLDRRT 60
Query: 104 KTPCGFCFALFYSREDTEDAVKYISGTILDDRPIRVDF 141
G+ + + ++ + A++ ++G L +PI VD+
Sbjct: 61 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>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 = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 50/98 (51%), Gaps = 5/98 (5%)
Query: 44 SAYRDRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNS 103
S +D PG Q E +L T V+ TEE I++ F+ GEIK I + LD+ +
Sbjct: 7 SVEQDGDEPGPQRSVEGWILFVTGVHE-----EATEEDIHDKFAEYGEIKNIHLNLDRRT 61
Query: 104 KTPCGFCFALFYSREDTEDAVKYISGTILDDRPIRVDF 141
G+ + + ++ + A++ ++G L +PI VD+
Sbjct: 62 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
S+ +YVG++ F TE+ + +F G+I I++ D ++ G+ F F E A
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 124 VKYISGTILDDRPIRV 139
++ ++G L RP+RV
Sbjct: 64 LEQLNGFELAGRPMRV 79
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKT---PCGFCFALFYSREDT 120
S+ +++ N++F TTEE + +FS+ G IK + KN GF F + E
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 121 EDAVKYISGTILDDRPIRV 139
+ A+K + G +D + V
Sbjct: 64 QKALKQLQGHTVDGHKLEV 82
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 52 PGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCF 111
PG Q E +L T V+ TEE I++ F+ GEIK I + LD+ + G+
Sbjct: 1 PGPQRSVEGWILFVTGVHE-----EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 55
Query: 112 ALFYSREDTEDAVKYISGTILDDRPIRVDF 141
+ + ++ + A++ ++G L +PI VD+
Sbjct: 56 VEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 63 LASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDK-NSKTPCGFCFALFYSREDTE 121
+ T V++G ++ T++ I E+FS G+IK I M +++ + G+ + F + ++ E
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 122 DAVKYISGTILDDRPI 137
A+K++ G +D + I
Sbjct: 62 KALKHMDGGQIDGQEI 77
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
++YVG++ TE +YE FS AG I I + D ++ G+ + F D E A+
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 126 YISGTILDDRPIRV 139
++ ++ +P+R+
Sbjct: 71 TMNFDVIKGKPVRI 84
Score = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+++ N+ + +Y+ FS G I + D+N G+ F F ++E E A++
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK 157
Query: 127 ISGTILDDRPIRV 139
++G +L+DR + V
Sbjct: 158 MNGMLLNDRKVFV 170
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
++V N+S+ ++EE + +LFS G + ++ +D +K P GF F F E A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 128 SGTILDDRPIRV 139
G + R + V
Sbjct: 71 DGQVFQGRMLHV 82
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
S VY+G++ + TEEQI +L S G + + M D + G+ F F E + A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 124 VKYISGTILDDR 135
V+ ++G L R
Sbjct: 63 VRNLNGYQLGSR 74
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
T+YVGN+S TE I +LFS+ G K M + S P +CF FY D A+
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 74
Query: 127 ISGTILDDRPIRVDF 141
++G + + ++V++
Sbjct: 75 MNGRKILGKEVKVNW 89
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
++YVG++ TE +YE FS AG I I + D ++ G+ + F D E A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 126 YISGTILDDRPIRV 139
++ ++ +P+R+
Sbjct: 76 TMNFDVIKGKPVRI 89
Score = 33.9 bits (76), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+++ N+ + +Y+ FS G I + D+N G+ F F ++E E A++
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK 162
Query: 127 ISGTILDDRPIRV 139
++G +L+DR + V
Sbjct: 163 MNGMLLNDRKVFV 175
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
VYVGN+ + ++ FS G ++ + + ++ P GF F F D EDAV+ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRGL 57
Query: 128 SGTILDDRPIRVDFDWGF 145
G ++ +RV+ G
Sbjct: 58 DGKVICGSRVRVELSTGM 75
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
T YVGN+ F T + I +F I+ + + DK++ GFC+ F + ++A+ Y
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75
Query: 127 ISGTILDDRPIRVDFDWG 144
G +L DR +RVD G
Sbjct: 76 -DGALLGDRSLRVDIAEG 92
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
S VY+G++ + TEEQI +L S G + + M D + G+ F F E + A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 124 VKYISGTILDDR 135
V+ ++G L R
Sbjct: 61 VRNLNGYQLGSR 72
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 39/74 (52%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
V+VG++S T E I F+ G+I + D + G+ F FY++ D E+A+ ++
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 128 SGTILDDRPIRVDF 141
G L R IR ++
Sbjct: 78 GGQWLGGRQIRTNW 91
>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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
S VY+G++ + TEEQI +L S G + + M D + G+ F F E + A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 124 VKYISGTILDDRPIRVDF 141
V+ ++G L R ++ +
Sbjct: 62 VRNLNGYQLGSRFLKCGY 79
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+YVGN+ TE+ + + F G I I + +DKN+K + F ++ D A++
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKN-VNYAFVEYHQSHDANIALQT 60
Query: 127 ISGTILDDRPIRVDFDWGF 145
++G +++ +++ +W F
Sbjct: 61 LNGKQIENNIVKI--NWAF 77
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 3/88 (3%)
Query: 52 PGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCF 111
P + EE +E + +VYVGN+ + +T + + FS G I +I + DK S P G+ +
Sbjct: 25 PLSAEEKKE--IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAY 82
Query: 112 ALFYSREDTEDAVKYISGTILDDRPIRV 139
F R ++ DA + T+ R I+V
Sbjct: 83 IEFAER-NSVDAAVAMDETVFRGRTIKV 109
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 60 EALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSRED 119
E + + V N+ F ++ I ELF+ G +KK + D++ ++ G F R D
Sbjct: 83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRAD 141
Query: 120 TEDAVKYISGTILDDRPIRVDF 141
A+K G LD RP+ +
Sbjct: 142 ALKAMKQYKGVPLDGRPMDIQL 163
>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 = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 42/74 (56%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
++V + TEE I++ F+ GEIK I + LD+ + G+ + + ++ + A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 128 SGTILDDRPIRVDF 141
+G L +PI VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 10/83 (12%)
Query: 59 EEALLASTTVYVGNMSFYTTEEQIYELFS--RAGEIKKIIMGLDKNSKTPCGFCFALFYS 116
E+ + + +YV N+ T+EE I + F+ + G ++++ K + F F +
Sbjct: 9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV--------KKIRDYAFVHFSN 60
Query: 117 REDTEDAVKYISGTILDDRPIRV 139
RED +A+K ++G +LD PI V
Sbjct: 61 REDAVEAMKALNGKVLDGSPIEV 83
>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 = 7e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 42/74 (56%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
++V + TEE I++ F+ GEIK I + LD+ + G+ + + ++ + A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 128 SGTILDDRPIRVDF 141
+G L +PI VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 42/74 (56%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
++V + TEE I++ F+ GEIK I + LD+ + G+ + + ++ + A++ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 128 SGTILDDRPIRVDF 141
+G L +PI VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 60 EALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSRED 119
E + + V N+ F ++ I ELF+ G +KK + D++ ++ G F R D
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRAD 88
Query: 120 TEDAVKYISGTILDDRPIRV 139
A+K G LD RP+ +
Sbjct: 89 ALKAMKQYKGVPLDGRPMDI 108
>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 = 8e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+YVG++ F TE+ + +F G I+ I + +D + G+ F F E + A++ +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 128 SGTILDDRPIRV 139
+G L RP++V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 60 EALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSRED 119
E + + V N+ F ++ I ELF+ G +KK + D++ ++ G F R D
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRAD 88
Query: 120 TEDAVKYISGTILDDRPIRV 139
A+K G LD RP+ +
Sbjct: 89 ALKAMKQYKGVPLDGRPMDI 108
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+ V N+ F ++ I ELF+ G +KK + D++ ++ G F + D A+K
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS-LGTADVHFERKADALKAMKQY 89
Query: 128 SGTILDDRPIRV 139
+G LD RP+ +
Sbjct: 90 NGVPLDGRPMNI 101
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
TV++ N+SF + EE + E+ + G++K + + L +++ G FA F ++E + +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 127 IS------GTILDDRPIRVDF 141
S G LD R ++VD
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDL 97
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSRE 118
++VG +S T EE+I E F GE++ I + +D + GFCF F E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 4/78 (5%)
Query: 65 STTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV 124
S T+ + N+S+ TEE + E+F +A IK + ++N K+ G+ F F S ED ++A+
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSK-GYAFIEFASFEDAKEAL 70
Query: 125 KYISGTILDDRPIRVDFD 142
+ ++ R IR++
Sbjct: 71 NSCNKREIEGRAIRLELQ 88
>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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTE 121
++VG +S T EE+I E F GE++ I + +D + GFCF F E +
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 57
>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 = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+ V N+ F ++ I ELF+ G +KK + D++ ++ G F + D A K
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS-LGTADVHFERKADALKAXKQY 90
Query: 128 SGTILDDRPIRV 139
+G LD RP +
Sbjct: 91 NGVPLDGRPXNI 102
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+Y+ N+ + T E++Y++F + G I++I +G N+ G + ++ D ++AV ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 128 SGTILDDR 135
SG + +R
Sbjct: 68 SGFNVSNR 75
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 63 LASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTED 122
L S +++ N+ + +Y+ FS G I + D+N G+ F F ++E E
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAER 60
Query: 123 AVKYISGTILDDRPIRV 139
A++ ++G +L+DR + V
Sbjct: 61 AIEKMNGMLLNDRKVFV 77
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 65 STTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV 124
+TV+V N+ + +++ E+FS AG + + + DK+ K+ G F + A+
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS-RGIGTVTFEQSIEAVQAI 73
Query: 125 KYISGTILDDRPIRVDFD 142
+G +L DRP+ V D
Sbjct: 74 SMFNGQLLFDRPMHVKMD 91
>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 = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 39/76 (51%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
T + V + T++++ LFS GE++ + DK + G+ F + + +D E A+
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 126 YISGTILDDRPIRVDF 141
++G L + I+V +
Sbjct: 80 TLNGLRLQSKTIKVSY 95
>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 = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 39/76 (51%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
T + V + T++++ LFS GE++ + DK + G+ F + + +D E A+
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 126 YISGTILDDRPIRVDF 141
++G L + I+V +
Sbjct: 65 TLNGLRLQSKTIKVSY 80
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
++YVGN+ + T E++ F G + ++ + DK S P GF + F +E ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 65
Query: 127 ISGTILDDRPIRV 139
+ ++ R I+V
Sbjct: 66 LDESLFRGRQIKV 78
>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 = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+++G +SF TT+E + F + G + ++ D N+K GF F + + E+ + A
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 64
Query: 128 SGTILDDRPIRVD 140
++ RP +VD
Sbjct: 65 ----MNARPHKVD 73
Score = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 39 DQRKLSAYRDRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMG 98
+ ++ + D + PG A L ++VG + T E + + F + G+I+ I +
Sbjct: 78 EPKRAVSREDSQRPG-------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 130
Query: 99 LDKNSKTPCGFCFALFYSREDTEDAVKYI 127
D+ S GF F F D D+V I
Sbjct: 131 TDRGSGKKRGFAFVTF----DDHDSVDKI 155
>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 = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSRE 118
++YVGN+ + T E++ F G + ++ + DK S P GF + F +E
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+++G +SF TT+E + F + G + ++ D N+K GF F + + E+ + A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 71
Query: 128 SGTILDDRPIRVD 140
++ RP +VD
Sbjct: 72 ----MNARPHKVD 80
Score = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 39 DQRKLSAYRDRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMG 98
+ ++ + D + PG A L ++VG + T E + + F + G+I+ I +
Sbjct: 85 EPKRAVSREDSQRPG-------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 137
Query: 99 LDKNSKTPCGFCFALFYSREDTEDAVKYI 127
D+ S GF F F D D+V I
Sbjct: 138 TDRGSGKKRGFAFVTF----DDHDSVDKI 162
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+++G +SF TT+E + F + G + ++ D N+K GF F + + E+ + A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 71
Query: 128 SGTILDDRPIRVD 140
++ RP +VD
Sbjct: 72 ----MNARPHKVD 80
Score = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 39 DQRKLSAYRDRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMG 98
+ ++ + D + PG A L ++VG + T E + + F + G+I+ I +
Sbjct: 85 EPKRAVSREDSQRPG-------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 137
Query: 99 LDKNSKTPCGFCFALFYSREDTEDAVKYI 127
D+ S GF F F D D+V I
Sbjct: 138 TDRGSGKKRGFAFVTF----DDHDSVDKI 162
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+++G +SF TT+E + F + G + ++ D N+K GF F + + E+ + A
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 70
Query: 128 SGTILDDRPIRVD 140
++ RP +VD
Sbjct: 71 ----MNARPHKVD 79
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 39 DQRKLSAYRDRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMG 98
+ ++ + D + PG A L ++VG + T E + + F + G+I+ I +
Sbjct: 84 EPKRAVSREDSQRPG-------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 136
Query: 99 LDKNSKTPCGFCFALFYSREDTEDAVKYI 127
D+ S GF F F D D+V I
Sbjct: 137 TDRGSGKKRGFAFVTF----DDHDSVDKI 161
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+++G +SF TT+E + F + G + ++ D N+K GF F + + E+ + A
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 72
Query: 128 SGTILDDRPIRVD 140
++ RP +VD
Sbjct: 73 ----MNARPHKVD 81
Score = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 4/67 (5%)
Query: 61 ALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDT 120
A L ++VG + T E + + F + G+I+ I + D+ S GF F F D
Sbjct: 101 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF----DD 156
Query: 121 EDAVKYI 127
D+V I
Sbjct: 157 HDSVDKI 163
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+++G +SF TT+E + F + G + ++ D N+K GF F + + E+ + A
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---- 69
Query: 128 SGTILDDRPIRVD 140
++ RP +VD
Sbjct: 70 ----MNARPHKVD 78
Score = 31.2 bits (69), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 39 DQRKLSAYRDRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMG 98
+ ++ + D + PG A L ++VG + T E + + F + G+I+ I +
Sbjct: 83 EPKRAVSREDSQRPG-------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 135
Query: 99 LDKNSKTPCGFCFALFYSREDTEDAVKYI 127
D+ S GF F F D D+V I
Sbjct: 136 TDRGSGKKRGFAFVTF----DDHDSVDKI 160
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEI---KKIIMGLD-KNSKTPCGFCFALFYSRED 119
S+ +++GN+ E+ +Y+ FS G I KI+ D NSK G+ F F S +
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSK---GYAFINFASFDA 60
Query: 120 TEDAVKYISGTILDDRPIRVDF 141
++ A++ ++G L +RPI V +
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSY 82
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 39/76 (51%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
T + V + T++++ LFS GE++ + DK + G+ F + + +D E A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 126 YISGTILDDRPIRVDF 141
++G L + I+V +
Sbjct: 63 TLNGLRLQSKTIKVSY 78
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 62 LLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTE 121
++ +Y+ + T++ + ++FSR G I + +D+ + G F F R + E
Sbjct: 85 VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAE 144
Query: 122 DAVKYISG--TILDDRPIRVDF 141
+A+ +G PI V F
Sbjct: 145 EAITSFNGHKPPGSSEPITVXF 166
>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 = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 39/76 (51%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
T + V + T++++ LFS GE++ + DK + G+ F + + +D E A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 126 YISGTILDDRPIRVDF 141
++G L + I+V +
Sbjct: 63 TLNGLRLQSKTIKVSY 78
Score = 30.8 bits (68), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 62 LLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTE 121
++ +Y+ + T++ + ++FSR G I + +D+ + G F F R + E
Sbjct: 85 VIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAE 144
Query: 122 DAVKYISG--TILDDRPIRVDF 141
+A+ +G PI V F
Sbjct: 145 EAITSFNGHKPPGSSEPITVKF 166
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
VYVGN+ + ++ F G ++ + + ++ P GF F F D DAV+ +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVREL 130
Query: 128 SGTILDDRPIRVDFDWG 144
G L +RV+ G
Sbjct: 131 DGRTLCGCRVRVELSNG 147
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
A+ T+ N+SF TE+++ E+F A EI+ ++ D SK G + F S D E
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFEDALEIR--LVSQDGKSK---GIAYIEFKSEADAEKN 69
Query: 124 VKYISGTILDDRPI 137
++ G +D R +
Sbjct: 70 LEEKQGAEIDGRSV 83
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+++G +S+ TT+E + E F + GE+K+ ++ D +K GF F F + D V
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV-DKVLAQ 61
Query: 128 SGTILDDRPI 137
S LD + I
Sbjct: 62 SRHELDSKTI 71
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
VYVGN+ + ++ F G ++ + + ++ P GF F F D DAV+ +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRDL 130
Query: 128 SGTILDDRPIRVDFDWG 144
G L +RV+ G
Sbjct: 131 DGRTLCGCRVRVELSNG 147
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
A+ T+ N+SF TE+++ E+F A EI+ ++ D SK G + F S D E
Sbjct: 98 AARTLLAKNLSFNITEDELKEVFEDALEIR--LVSQDGKSK---GIAYIEFKSEADAEKN 152
Query: 124 VKYISGTILDDRPI 137
++ G +D R +
Sbjct: 153 LEEKQGAEIDGRSV 166
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 35.0 bits (79), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+++G +S+ TT+E + E F + GE+K+ ++ D +K GF F F + D V
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV-DKVLAQ 86
Query: 128 SGTILDDRPI 137
S LD + I
Sbjct: 87 SRHELDSKTI 96
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 35.0 bits (79), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
T ++VG + ++TT+ + + F G+I++ ++ D+ + G+ F R E A K
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 126 YISGTILDDRPIRVDFDW 143
+ I+D R V+ +
Sbjct: 78 DPN-PIIDGRKANVNLAY 94
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 34.7 bits (78), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+YVGN+ + I ++F + G I+ I + KN + F F F D EDAV
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 128 SGTILDDRPIRVDF 141
G D +RV+F
Sbjct: 82 DGYDYDGYRLRVEF 95
>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 = 34.3 bits (77), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+Y+ N+ + T E++Y++F + G I++I +G N+ G + ++ D ++A ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 128 SG 129
SG
Sbjct: 78 SG 79
>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 = 34.3 bits (77), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%)
Query: 64 ASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
+ T + V + T+E+ LF GEI+ + DK + G+ F + +D E A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 124 VKYISGTILDDRPIRVDF 141
+ ++G L + I+V +
Sbjct: 61 INTLNGLRLQTKTIKVSY 78
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 61 ALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDT 120
A + +YV + T++++ +LFS+ G I + +D+ + G F F R +
Sbjct: 84 ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143
Query: 121 EDAVKYISGTILDD--RPIRVDF 141
E+A+K ++G PI V F
Sbjct: 144 EEAIKGLNGQKPSGATEPITVKF 166
>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 = 34.3 bits (77), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY- 126
+++G +S+ TT++ + + FS+ GE+ + LD + GF F LF E + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 127 ---ISGTILDDR 135
++G ++D +
Sbjct: 62 EHKLNGKVIDPK 73
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 34.3 bits (77), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+++ N+ + +Y+ FS G I + D+N G+ F F ++E E A++
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK 70
Query: 127 ISGTILDDRPIRV 139
++G +L+DR + V
Sbjct: 71 MNGMLLNDRKVFV 83
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 34.3 bits (77), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+Y+ N+ + T E++Y++F + G I++I +G N+ G + ++ D ++A ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 128 SG 129
SG
Sbjct: 72 SG 73
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.9 bits (76), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 53 GTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPC--GFC 110
GT + ++ L + ++VG + +E+ + ELF + G + +I + D++ P G C
Sbjct: 3 GTLDHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCC 62
Query: 111 FALFYSREDTEDA 123
F FY+R+ +A
Sbjct: 63 FVTFYTRKAALEA 75
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIK--KIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
+++G +S TE I +FS G+I+ +I+ G D S+ G F F +R + A+K
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR---GCAFVTFTTRAMAQTAIK 166
Query: 126 YI 127
+
Sbjct: 167 AM 168
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 33.9 bits (76), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 44/94 (46%), Gaps = 5/94 (5%)
Query: 48 DRRFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPC 107
D PG Q E +L T+++ E++I E F GEIK I + LD+ +
Sbjct: 14 DELEPGPQRSVEGWILFVTSIHE-----EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 68
Query: 108 GFCFALFYSREDTEDAVKYISGTILDDRPIRVDF 141
G+ + + + A + ++G + + I+VD+
Sbjct: 69 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 33.9 bits (76), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 58 FEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSR 117
E + TV+VG + E +I F+R G +K++ + D+ + G+ F FY+
Sbjct: 2 LPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVS-KGYGFVSFYND 60
Query: 118 EDTEDAVK 125
D + V+
Sbjct: 61 VDVQKIVE 68
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 33.5 bits (75), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
++VG + + TT+E + FS+ GE+ ++ DK + GF F F
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN--------C 70
Query: 128 SGTILDDRPIRVD 140
GT+L RP +D
Sbjct: 71 VGTVLASRPHTLD 83
>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 = 33.5 bits (75), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+YVG ++ ++ ++ F G+I I + LD ++ GF F F ED A+
Sbjct: 4 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 127 ISGTILDDRPIRVDF 141
++ + L R IRV+
Sbjct: 64 MNESELFGRTIRVNL 78
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 33.5 bits (75), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV 124
+++G +SF TTEE + + + G++ ++ D SK GF F F S + + A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 33.5 bits (75), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 60 EALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSRED 119
E + TV+VG + E +I F+R G +K++ + D+ G+ F FY+ D
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVD 62
Query: 120 TEDAVK 125
+ V+
Sbjct: 63 VQKIVE 68
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV 124
++VG + E ++ E F + G + +++M D + P GF F F + + AV
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+YVG ++ ++ ++ F G+I I + LD ++ GF F F ED A+
Sbjct: 7 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 127 ISGTILDDRPIRVDF 141
++ + L R IRV+
Sbjct: 67 MNESELFGRTIRVNL 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 = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+YVG ++ ++ ++ F G+I I + LD ++ GF F F ED A+
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 127 ISGTILDDRPIRVDF 141
++ + L R IRV+
Sbjct: 69 MNESELFGRTIRVNL 83
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
+YVG ++ ++ ++ F G+I I + LD ++ GF F F ED A+
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 127 ISGTILDDRPIRVDF 141
++ + L R IRV+
Sbjct: 125 MNESELFGRTIRVNL 139
>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 = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 5/90 (5%)
Query: 52 PGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCF 111
PG Q E +L T+++ E++I E F GEIK I + LD+ + G+
Sbjct: 64 PGPQRSVEGWILFVTSIHE-----EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118
Query: 112 ALFYSREDTEDAVKYISGTILDDRPIRVDF 141
+ + + A + ++G + + I+VD+
Sbjct: 119 VEYETHKQALAAKEALNGAEIMGQTIQVDW 148
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 16/89 (17%)
Query: 50 RFPGTQEEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGF 109
R PG E+ + ++VGN+ TEE++ +LF + G+ ++ + DK GF
Sbjct: 12 RKPG-----EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GF 60
Query: 110 CFALFYSREDTEDAVKYISGTILDDRPIR 138
F +R E I+ LD+ P+R
Sbjct: 61 GFIRLETRTLAE-----IAKVELDNMPLR 84
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
+YVG ++ ++ ++ F G+I I + LD ++ GF F F ED A+ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 128 SGTILDDRPIRVDF 141
+ + L R IRV+
Sbjct: 75 NESELFGRTIRVNL 88
>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 = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 59 EEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSRE 118
E+ + ++VGN+ TEE++ +LF + G+ ++ + DK GF F +R
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRT 62
Query: 119 DTEDAVKYISGTILDDRPIRVDF 141
E A + L + +RV F
Sbjct: 63 LAEIAKVELDNMPLRGKQLRVRF 85
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 44/88 (50%), Gaps = 10/88 (11%)
Query: 55 QEEFEEALLAST----TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFC 110
Q FE+ + S+ TVY G ++ T++ + + FS G+I +I + +K G+
Sbjct: 11 QLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYS 64
Query: 111 FALFYSREDTEDAVKYISGTILDDRPIR 138
F F + E A+ ++GT ++ ++
Sbjct: 65 FVRFSTHESAAHAIVSVNGTTIEGHVVK 92
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
+YV + +++++ +LFS+ G I + LD+ + G F F R + E+A+K
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 126 YISG--TILDDRPIRVDF 141
++G + PI V F
Sbjct: 62 GLNGQKPLGAAEPITVKF 79
>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 = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 69 YVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYIS 128
+VG +S+ T+++ + + F++ GE+ + D N+ GF F LF E
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE------- 67
Query: 129 GTILDDRPIRVD 140
+LD + R+D
Sbjct: 68 -KVLDQKEHRLD 78
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 63 LASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTED 122
+ TV+VG + E +I F+R G +K++ + D+ + G+ F FY+ D +
Sbjct: 8 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSK-GYGFVSFYNDVDVQK 66
Query: 123 AVK 125
V+
Sbjct: 67 IVE 69
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 31.6 bits (70), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTE 121
++VG +S TT E + F + G++ ++ DK + GF F F S + E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVE 55
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 31.6 bits (70), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 67 TVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKY 126
T+ N+ + T++++ E+F A EI+ ++ D SK G + F + D E +
Sbjct: 95 TLLAKNLPYKVTQDELKEVFEDAAEIR--LVSKDGKSK---GIAYIEFKTEADAEKTFEE 149
Query: 127 ISGTILDDRPI 137
GT +D R I
Sbjct: 150 KQGTEIDGRSI 160
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 61 ALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDT 120
A + +YV + +++++ +LFS+ G I + LD+ + G F F R +
Sbjct: 86 ASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEA 145
Query: 121 EDAVKYISG--TILDDRPIRVDF 141
E+A+K ++G + PI V F
Sbjct: 146 EEAIKGLNGQKPLGAAEPITVKF 168
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 65 STTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPC--GFCFALFYSREDTED 122
+ ++VG + +E+ + ELF + G + +I + D++ P G CF FY+R+ +
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 123 A 123
A
Sbjct: 63 A 63
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 65 STTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPC--GFCFALFYSREDTED 122
++ + V N+ F + +I ELFS GE+K + + K + T GF F F +++D +
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRL-PKKMTGTGAHRGFGFVDFITKQDAKK 73
Query: 123 A 123
A
Sbjct: 74 A 74
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 30.8 bits (68), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPC--GFCFALFYSREDTEDA 123
++VG + +E+ + ELF + G + +I + D++ P G CF FY+R+ +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIK--KIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
+++G +S TE I +FS G+I+ +I+ G D S+ G F F +R + A+K
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSR---GCAFVTFTTRAMAQTAIK 154
Query: 126 YI 127
+
Sbjct: 155 AM 156
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 30.4 bits (67), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 65 STTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV 124
S +++G +++ TTE+ + E F + G + + + D + GF F F ++ V
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 125 K---YISGTILDDR 135
K + G ++D +
Sbjct: 63 KTQHILDGKVIDPK 76
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 30.4 bits (67), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 69 YVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPC--GFCFALFYSREDTEDA 123
+VG + +E+ + ELF + G + +I + D++ P G CF FY+R+ +A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIK--KIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
+++G +S TE I FS G+I+ +I+ G D S+ G F F +R + A+K
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSR---GCAFVTFTTRAXAQTAIK 154
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVK 125
TT Y+GN+ + TE + LF G I LD G CF + + E +
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFI------LDFKHYPEKGCCFIKYDTHEQAAVCIV 81
Query: 126 YISGTILDDRPIRVDFDWG 144
++ R +R WG
Sbjct: 82 ALANFPFQGRNLRT--GWG 98
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV- 124
TT+YVG + TE + F + GEI+ I + + C F F +R+ E A
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITV----VQRQQC--AFIQFATRQAAEVAAE 66
Query: 125 KYISGTILDDRPIRVDFDWG 144
K + I++ R R++ WG
Sbjct: 67 KSFNKLIVNGR--RLNVKWG 84
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 65 STTVYVGNMSFYTTEEQIYELFSRAGE-IKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
+ ++++G++ Y E I F+ GE + + + ++ + P G+CF F E
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 124 VKYISGTILD 133
+ I+G L
Sbjct: 69 LHKINGKPLP 78
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 68 VYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYI 127
++VGN+S T +++ LF R G + + + D + F D + A+ +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 128 SGTILDDRPIRVDF 141
+G + + I V+
Sbjct: 64 NGKEVKGKRINVEL 77
>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 = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 3/98 (3%)
Query: 30 LSAMASLFKDQRKLSAYRDRRFPGTQ---EEFEEALLASTTVYVGNMSFYTTEEQIYELF 86
L M S+ R + R Q ++ E A +YV ++ +++ I +F
Sbjct: 72 LEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 131
Query: 87 SRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV 124
G+IK + D + G+ F + + ++DAV
Sbjct: 132 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 26.9 bits (58), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 27/55 (49%)
Query: 79 EEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYISGTILD 133
++ + LFS+AG++ + +D+ + GF F S D + +K G LD
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 3/98 (3%)
Query: 30 LSAMASLFKDQRKLSAYRDRRFPGTQ---EEFEEALLASTTVYVGNMSFYTTEEQIYELF 86
L M S+ R + R Q ++ E A +YV ++ +++ I +F
Sbjct: 87 LEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 146
Query: 87 SRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAV 124
G+IK + D + G+ F + + ++DAV
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
>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 = 26.9 bits (58), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 32/69 (46%)
Query: 56 EEFEEALLASTTVYVGNMSFYTTEEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFY 115
++ E A +YV ++ +++ I +F G+IK + D + G+ F +
Sbjct: 100 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Query: 116 SREDTEDAV 124
+ ++DAV
Sbjct: 160 KAQSSQDAV 168
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 27/55 (49%)
Query: 79 EEQIYELFSRAGEIKKIIMGLDKNSKTPCGFCFALFYSREDTEDAVKYISGTILD 133
++ + LFS+AG++ + +D+ + GF F S D + +K G LD
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 26.9 bits (58), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 14/76 (18%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 66 TTVYVGNMSFYTTEEQIYELFSRAG--EIKKIIMGLDKNSKTPCGFCFALFYSREDTEDA 123
VYVG+ S++TT++Q+ ++ G ++ ++ ++ + G+ + S
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL 115
Query: 124 VKYISGTILDDRPIRV 139
++ + G +L+ + V
Sbjct: 116 LELLPGKVLNGEKVDV 131
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
0.324 0.139 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,841,450
Number of Sequences: 62578
Number of extensions: 217895
Number of successful extensions: 758
Number of sequences better than 100.0: 123
Number of HSP's better than 100.0 without gapping: 105
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 627
Number of HSP's gapped (non-prelim): 139
length of query: 216
length of database: 14,973,337
effective HSP length: 95
effective length of query: 121
effective length of database: 9,028,427
effective search space: 1092439667
effective search space used: 1092439667
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)