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= 020297
(328 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 3/82 (3%)
Query: 219 DNPPCNTLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSASSVH 278
+NPP + LF+ NL E NE L LF+ PGFK+++++ RH + F+EF++ A +
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV-PGRHDIAFVEFDNEVQAGAAR 261
Query: 279 HNLQGAVIPSSGSVGMRIQYSK 300
LQG I + + M+I ++K
Sbjct: 262 DALQGFKITQNNA--MKISFAK 281
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 52 IFITGLPDDVKERELQNLLRWLPGYEASQVNYKGEKPMGFALFSTAQLAVAAKDALQEMI 111
+F+T LP++ E L L PG++ ++ G + F F A AA+DALQ
Sbjct: 210 LFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFDNEVQAGAARDALQG-- 266
Query: 112 FDAETKSVLHTEMAKK 127
F + + AKK
Sbjct: 267 FKITQNNAMKISFAKK 282
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 3/82 (3%)
Query: 219 DNPPCNTLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSASSVH 278
+NPP + LF+ NL E NE L LF+ PGFK+++++ RH + F+EF++ A +
Sbjct: 9 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV-PGRHDIAFVEFDNEVQAGAAR 67
Query: 279 HNLQGAVIPSSGSVGMRIQYSK 300
LQG I + + M+I ++K
Sbjct: 68 DALQGFKITQNNA--MKISFAK 87
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 52 IFITGLPDDVKERELQNLLRWLPGYEASQVNYKGEKPMGFALFSTAQLAVAAKDALQEMI 111
+F+T LP++ E L L PG++ ++ G + F F A AA+DALQ
Sbjct: 16 LFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFDNEVQAGAARDALQG-- 72
Query: 112 FDAETKSVLHTEMAKK 127
F + + AKK
Sbjct: 73 FKITQNNAMKISFAKK 88
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 219 DNPPCNTLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSASSVH 278
+ PP LF+ NL E NE L LF+ PGFK+++++ RH + F+EF +++
Sbjct: 4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-RHDIAFVEFTTELQSNAAK 62
Query: 279 HNLQGAVIPSSGSVGMRIQYSK 300
LQG I + + M+I ++K
Sbjct: 63 EALQGFKI--TPTHAMKITFAK 82
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 50 RTIFITGLPDDVKERELQNLLRWLPGYEASQVNYKGEKPMGFALFSTAQLAVAAKDALQ 108
+ +F+T LP++ E L L PG++ ++ + F F+T + AAK+ALQ
Sbjct: 9 QILFLTNLPEETNEMMLSMLFNQFPGFKEVRL-VPNRHDIAFVEFTTELQSNAAKEALQ 66
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 220 NPPCNTLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQER----HTVCFIEFEDVNSAS 275
NPP +++G++ EE++ L S +K++ + FIEF D+ S++
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 276 SVHHNLQGAVIPSSGSVGMRIQYSKN 301
S NL G + GS ++ YS N
Sbjct: 61 SAVRNLNGYQL---GSRFLKCGYSSN 83
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 221 PPCNTLFIGNLGESINEEELRGLFSAQPG-FKQMKVLRQERHTVCFIEFEDVNSA 274
PP TL + N+ S++EE+L+ LFS+ G K K +++R + I+ V A
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR-KMALIQMGSVEEA 202
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 218 KDNPPCNT-LFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSASS 276
+D+ P + +++GNLG + N+ EL F + + V R F+EFED A+
Sbjct: 67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-PGFAFVEFEDPRDAAD 125
Query: 277 VHHNLQGAVIPSSGSVGMRIQ 297
+L G + G R++
Sbjct: 126 AVRDLDGRTL-----CGCRVR 141
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 221 PPCNTLFIGNLGESINEEELRGLFSAQPG-FKQMKVLRQERHTVCFIEFEDVNSA 274
PP TL + N+ S++EE+L+ LFS+ G K K +++R + I+ V A
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR-KMALIQMGSVEEA 171
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 31.6 bits (70), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 7/81 (8%)
Query: 218 KDNPPCNT-LFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSASS 276
+D+ P + +++GNLG + N+ EL F + + V R F+EFED A+
Sbjct: 67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-PGFAFVEFEDPRDAAD 125
Query: 277 VHHNLQGAVIPSSGSVGMRIQ 297
L G + G R++
Sbjct: 126 AVRELDGRTL-----CGCRVR 141
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 9/89 (10%)
Query: 226 LFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSASSVHHNLQGAV 285
+++GNLG + EL FS + + + R F+EFED A L G V
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-GFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 286 IPSSG-----SVGM--RIQYSKNPFGKRK 307
I S S GM R ++ + P +RK
Sbjct: 62 ICGSRVRVELSTGMPRRSRFDRPP-ARRK 89
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 225 TLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSA 274
TL++G LG++I E +LR F + + V+ +R FI+F +A
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVV--QRQQCAFIQFATRQAA 61
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 7/68 (10%)
Query: 226 LFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHT-------VCFIEFEDVNSASSVH 278
LFI NL S EE L+G+FS K + +++ F+E++ A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 279 HNLQGAVI 286
LQG +
Sbjct: 68 KQLQGHTV 75
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 29.3 bits (64), Expect = 3.1, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 224 NTLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSASSVHHNLQG 283
N L+IGNL ++ ++LR LF + +VL + + F+++ D N A L G
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYA--FVDYPDQNWAIRAIETLSG 66
Query: 284 AV 285
V
Sbjct: 67 KV 68
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 224 NTLFIGNLGESINEEELRGLFS 245
+ LF+GNL I EEE+R LF
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFE 44
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 52 IFITGLPDDVKERELQNLLRWLPGYEASQVNYKGEKPMGFALFSTAQLAVAAKDALQEM 110
+F+ LP D+ E E++ L +A +V +K GF T LA AK L M
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM 81
>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 = 28.9 bits (63), Expect = 3.9, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 52 IFITGLPDDVKERELQNLLRWLPGYEASQVNYKGEKPMGFALFSTAQLAVAAKDALQEM 110
+F+ LP D+ E E++ L +A +V +K GF T LA AK L M
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM 74
Score = 28.9 bits (63), Expect = 4.6, Method: Composition-based stats.
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 226 LFIGNLGESINEEELRGLF 244
LF+GNL I EEE+R LF
Sbjct: 18 LFVGNLPPDITEEEMRKLF 36
>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 = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 225 TLFIGNLGESINEEELRGLFSAQPGFKQ----MKVLRQERHTVCFIEFEDVNSASSVHHN 280
TL++GNL EE++ LFS K+ + +++ CF+E+ A +
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 281 LQGAVIP 287
+ G +
Sbjct: 101 INGTRLD 107
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 28.5 bits (62), Expect = 5.0, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 226 LFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTVCFIEFEDVNSASSVHHNLQGAV 285
LFIGNL E+E+R LF + +++ F+ ED +A NL
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN----YGFVHIEDKTAAEDAIRNLHHYK 66
Query: 286 IPSSGSVGMRIQYSKN 301
+ V + ++ SKN
Sbjct: 67 L---HGVNINVEASKN 79
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 28.5 bits (62), Expect = 5.6, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 222 PCNTLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQER----HTVCFIEFEDVNSASSV 277
P +++G++ EE++ L S +K++ + FIEF D+ S++S
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 278 HHNLQGAVIPSSGSVGMRIQYSKN 301
NL G + GS ++ YS N
Sbjct: 61 VRNLNGYQL---GSRFLKCGYSSN 81
>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 = 28.5 bits (62), Expect = 5.9, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 225 TLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQERHTV---CFIEFEDVNSASSVHHNL 281
TL++GNL EE++ LFS K++ + + T CF+E+ A + +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 282 QG 283
G
Sbjct: 80 NG 81
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 28.5 bits (62), Expect = 6.0, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 225 TLFIGNLGESINEEEL-RGLFSAQPGFKQMKVLRQERHTV----CFIEFEDVNSASSVHH 279
+L++G+L ++E + R + +K++R + CF+EF D+ +A H
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 280 NLQGAVIPSS 289
+ G +P +
Sbjct: 71 KINGKPLPGA 80
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 28.1 bits (61), Expect = 6.1, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 222 PCNTLFIGNLGESINEEELRGLFSAQPGFKQMKVLRQER----HTVCFIEFEDVNSASSV 277
P +++G++ EE++ L S +K++ + FIEF D+ S++S
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 278 HHNLQGAVIPSSGSVGMRIQYSKN 301
NL G + GS ++ YS N
Sbjct: 62 VRNLNGYQL---GSRFLKCGYSSN 82
>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 = 28.1 bits (61), Expect = 6.8, Method: Composition-based stats.
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 224 NTLFIGNLGESINEEELRGLFSAQPGFKQMKVL 256
NT+F+G + ++E E+R F+ K++K++
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKII 42
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 28.1 bits (61), Expect = 7.3, Method: Composition-based stats.
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 224 NTLFIGNLGESINEEELRGLFSAQPGFKQMKVL 256
NT+F+G + ++E E+R F+ K++K++
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKII 43
>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 = 28.1 bits (61), Expect = 7.4, Method: Composition-based stats.
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 224 NTLFIGNLGESINEEELRGLFSAQPGFKQMKVL 256
NT+F+G + ++E E+R F+ K++K++
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKII 42
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
0.317 0.133 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,854,812
Number of Sequences: 62578
Number of extensions: 264741
Number of successful extensions: 602
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 580
Number of HSP's gapped (non-prelim): 36
length of query: 328
length of database: 14,973,337
effective HSP length: 99
effective length of query: 229
effective length of database: 8,778,115
effective search space: 2010188335
effective search space used: 2010188335
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)