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= psy13318
(100 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 41/72 (56%), Positives = 49/72 (68%), Gaps = 9/72 (12%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE-LSVVANSIFAPE----- 84
SKTNLIVNYLPQ MTQEE +SLF S+GE+ESCKL+RDK TG+ L + P+
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 85 ---LNGLHSQTE 93
LNGL QT+
Sbjct: 61 INTLNGLRLQTK 72
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 28/38 (73%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
NL V+ LP+TMTQ+E++ LFS G + + +++ D+ TG
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTG 127
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 32/43 (74%), Positives = 39/43 (90%)
Query: 30 ESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+SKTNLIVNYLPQ MTQ+E KSLF S+G++ESCKL+RDK TG+
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQ 44
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 32/43 (74%), Positives = 39/43 (90%)
Query: 30 ESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+SKTNLIVNYLPQ MTQ+E KSLF S+G++ESCKL+RDK TG+
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQ 44
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 28/39 (71%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
NL V+ LP+TM+Q+EM+ LFS G + + +++ D+ TG
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATG 129
>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 = 72.4 bits (176), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 31/42 (73%), Positives = 36/42 (85%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+TNLIVNYLPQ MTQ+E++SLFSS+GEVES KLIRDK G
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH 44
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 72.4 bits (176), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 31/42 (73%), Positives = 36/42 (85%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+TNLIVNYLPQ MTQ+E++SLFSS+GEVES KLIRDK G
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH 42
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 34/47 (72%), Gaps = 1/47 (2%)
Query: 26 PSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
PS+E K NL ++ LP+TMTQ++++ +FS G + + +++ D+TTG
Sbjct: 81 PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTG 127
>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 = 72.4 bits (176), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 31/42 (73%), Positives = 36/42 (85%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+TNLIVNYLPQ MTQ+E++SLFSS+GEVES KLIRDK G
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH 42
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 34/47 (72%), Gaps = 1/47 (2%)
Query: 26 PSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
PS+E K NL ++ LP+TMTQ++++ +FS G + + +++ D+TTG
Sbjct: 81 PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTG 127
>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 = 68.9 bits (167), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 30/40 (75%), Positives = 34/40 (85%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
TNLIVNYLPQ TQ+E++SLFSS+GEVES KLIRDK G
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGH 59
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVANSIFAPE------ 84
S TNLIVNYLPQ MT E+ +LF ++G + +C+++RD TG A F E
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 85 ---LNGLHSQTERSRKS 98
LNG+ + +R + S
Sbjct: 62 IKVLNGITVRNKRLKVS 78
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVANSIFAPE------ 84
S TNLIVNYLPQ MT E+ +LF ++G + +C+++RD TG A F E
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 85 ---LNGLHSQTERSRKS 98
LNG+ + +R + S
Sbjct: 62 IKVLNGITVRNKRLKVS 78
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 26 PSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVA 77
P E K TNL V LP+T+T +++ ++F G + ++RDK TG VA
Sbjct: 82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVA 134
>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 = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 21/41 (51%), Positives = 29/41 (70%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S TNLIVNYLPQ T E+ +LF ++G + +C++ RD TG
Sbjct: 13 SNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTG 53
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 26 PSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVA 77
P E K TNL V LP+T+T +++ ++F G + ++RDK TG VA
Sbjct: 93 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVA 145
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 28/39 (71%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
NL V+ LP+TM+Q+EM+ LFS G + + +++ D+ TG
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATG 40
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 26 PSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVA 77
P E K TNL V LP+T+T +++ ++F G + ++RDK TG VA
Sbjct: 6 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVA 58
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 26/37 (70%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
NL+VNY+P T+ + +++ LF G +ES K++ D+ T
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRET 80
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 30/47 (63%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
P+ + S ++ V +P T+E++K +FS VG V S +L+ D+ TG+
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGK 48
>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 = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 31/46 (67%), Gaps = 2/46 (4%)
Query: 29 EESKT--NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
EE++ + V + Q ++ +++KS+F + G+++SC L RD TTG+
Sbjct: 104 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGK 149
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
L V L + TQE ++S FS GEV C +++DKTT
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTT 54
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 31/46 (67%), Gaps = 2/46 (4%)
Query: 29 EESKT--NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
EE++ + V + Q ++ +++KS+F + G+++SC L RD TTG+
Sbjct: 105 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGK 150
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 10/70 (14%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIR--------DKTTGELSVVANSIFAPELN 86
L + LP+ T++E++SLF G+V C +I+ DKT E ++ ++ +L+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAI--RNLHHYKLH 68
Query: 87 GLHSQTERSR 96
G++ E S+
Sbjct: 69 GVNINVEASK 78
>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 = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 30/46 (65%), Gaps = 2/46 (4%)
Query: 29 EESKT--NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
EE++ + V + Q ++ +++KS+F + G+++S L RD TTG+
Sbjct: 120 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGK 165
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 28/41 (68%)
Query: 29 EESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
E+ TNL ++ LP +M ++E++++ G+V S +++RD +
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS 62
>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 = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 30 ESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+S L + LP + +++K L +S G +++ L++D TG
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATG 153
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 32.3 bits (72), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
N+ V L + T E++K LFS G+V + KLI D+ T
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRET 39
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.3 bits (72), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 32 KTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
++ L V LP +T+EEM+ LF G+ + +DK G
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFG 61
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
+L V LPQ ++ E ++ FS G+VE +I D
Sbjct: 97 ASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVD 131
>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 = 32.0 bits (71), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 32 KTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
++ L V LP +T+EEM+ LF G+ + +DK G
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFG 54
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
++LIV LP T++++K FS+ GEV ++ +D TG
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGH 55
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 32 KTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVANS---IFAPELNG 87
+ L V LP +T+E+ K LF GE + RD+ G + + + + I EL+G
Sbjct: 22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDG 80
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
S + + L TQE ++ F GEV+ C ++RD T
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLT 63
>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 = 31.2 bits (69), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 28 NEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
NEE V L +++++K F+ GEV C + D TG
Sbjct: 7 NEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTG 50
>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 = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
L + LP + +++K L +S G +++ L++D TG
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATG 135
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 22/32 (68%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIR 66
L + + + T+ +++ +FSS G++E C+++R
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILR 141
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 22/35 (62%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ V +P+T ++++++ LF G V ++RD++
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRS 52
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVANSIF 81
SK+ + V+ LP ++T ++ +FS G+V +++DK T + VA +F
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 22/32 (68%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIR 66
L + + + T+ +++ +FSS G++E C+++R
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILR 129
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 22/35 (62%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ V +P+T ++++++ LF G V ++RD++
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRS 40
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
L + LP + +++K L +S G +++ L++D TG
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATG 133
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
L + LP + +++K L +S G +++ L++D TG
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATG 40
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
T + V LP T ++ F G++E +I D+ TG+
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGK 57
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 24/39 (61%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
++ V L +T E++KS F+ G++ ++++D TG+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGK 55
>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 = 0.28, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 21/32 (65%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIR 66
L + + + T+ +++ FSS G++E C+++R
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILR 129
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 21/34 (61%)
Query: 36 IVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
V +P+T ++++++ LF G V ++RD++
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRS 40
>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 = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
L V LP ++TQ++ + L G +E C L+ + TG+
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 133
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+ L + L + T+E +K +FS VG ++SC + + K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKK 41
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
L V LP ++TQ++ + L G +E C L+ + TG+
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 135
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
L V LP ++TQ++ + L G +E C L+ + TG+
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 135
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
+ + L TQE ++ F GEV+ C ++RD T
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLT 38
>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 = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ + L T++++K FS GEV C L D TG
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITG 38
>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 = 29.3 bits (64), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 23/39 (58%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
++ V L +T E++K+ F+ G + ++++D TG+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGK 55
>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 = 28.5 bits (62), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 22/35 (62%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ V +P+T ++++++ LF G V ++RD++
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRS 40
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 24 QTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKL 64
Q P +++ + ++V +P Q E++ LFS+ GE+++ +L
Sbjct: 8 QVP-KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRL 47
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
L V L + +T+ + LFS +G +SCK+I + T+ +
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND 55
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
L V L +T++ ++ +F G +ES +L+ D TG
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETG 65
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ V + M + E++S F+ G V+ K+I D+T
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT 47
>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 = 2.1, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVANSIFA-PELNGLHSQTE 93
+ V + T +E++SLF G V C +++D + A++ A +LNG + +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGK 71
Query: 94 R 94
R
Sbjct: 72 R 72
>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 = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 44 MTQEEMKSLFSSVGEVESCKLIRDKT 69
M + E++S F+ G V+ K+I D+T
Sbjct: 21 MDETEIRSFFARYGSVKEVKIITDRT 46
>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 = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 22/44 (50%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
P + + V + M + E++S F+ G V+ K+I D+T
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT 46
>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 = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 20/34 (58%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
N+ + L +++ + + FS+ G + SCK++ D
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD 40
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 20/34 (58%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
N+ + L +++ + + FS+ G + SCK++ D
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD 46
>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 = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 20/34 (58%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
N+ + L +++ + + FS+ G + SCK++ D
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD 138
>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 = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 20/34 (58%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
N+ + L +++ + + FS+ G + SCK++ D
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD 133
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
+ V L T E++K F G+V+ L+ DKTT
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTT 37
>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 = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGEL 73
L V + + T+E++ F+ GE+++ L D+ TG L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 64
>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 = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGEL 73
L V + + T+E++ F+ GE+++ L D+ TG L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 63
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 25.8 bits (55), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGEL 73
L V + + T+E++ F+ GE+++ L D+ TG L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 48
>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 = 25.8 bits (55), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGEL 73
L V + + T+E++ F+ GE+++ L D+ TG L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 48
>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 = 25.8 bits (55), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGEL 73
L V + + T+E++ F+ GE+++ L D+ TG L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 50
>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 = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGEL 73
L V + + T+E++ F+ GE+++ L D+ TG L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 48
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 37 VNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
V L + + +++ LF G + L +DKTTG+
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQ 55
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 25.4 bits (54), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 24 QTPSNEESKT-----NLIVNYLPQTMTQEEMKSLFSSVGEV 59
+ P ++SK L+ LP +TQ+E+K +F E+
Sbjct: 80 EKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEI 120
>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 = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+P T+E++ L S+VG V + K++ D TG
Sbjct: 12 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGR 44
>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 = 25.0 bits (53), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+P T+E++ L S+VG V + K++ D TG
Sbjct: 11 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGR 43
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
0.308 0.122 0.321
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,030,662
Number of Sequences: 62578
Number of extensions: 59595
Number of successful extensions: 240
Number of sequences better than 100.0: 72
Number of HSP's better than 100.0 without gapping: 68
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 162
Number of HSP's gapped (non-prelim): 82
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)