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= 026189
(242 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 = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 140 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 199
+++LF+ LP + +S LF F G++E+R++ P R + FVEFD+ A
Sbjct: 207 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV---PGRHD-----IAFVEFDNEVQAG 258
Query: 200 TAMDALHGYKFDDKKPDSPTLKIQFA 225
A DAL G+K +KI FA
Sbjct: 259 AARDALQGFKITQNN----AMKISFA 280
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 140 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 199
+++LF+ LP + +S LF F G++E+R++ P R + FVEFD+ A
Sbjct: 13 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV---PGRHD-----IAFVEFDNEVQAG 64
Query: 200 TAMDALHGYKFDDKKPDSPTLKIQFA 225
A DAL G+K +KI FA
Sbjct: 65 AARDALQGFKITQNN----AMKISFA 86
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 44/88 (50%), Gaps = 16/88 (18%)
Query: 140 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 199
+ +LF+ LP + +S LF F G++E+R++ P R + FVEF +
Sbjct: 8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLV---PNRHD-----IAFVEFTTELQSN 59
Query: 200 TAMDALHGYKFDDKKPDSPT--LKIQFA 225
A +AL G+K +PT +KI FA
Sbjct: 60 AAKEALQGFKI------TPTHAMKITFA 81
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 11/71 (15%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
LFV P D E++ +F PF +E+++++ FVEF++ + A A+
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----------FAFVEFEEAESAAKAI 82
Query: 203 DALHGYKFDDK 213
+ +HG F ++
Sbjct: 83 EEVHGKSFANQ 93
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.0 bits (84), Expect = 0.009, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 11/71 (15%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
LFV P D E++ +F PF +E+++++ FVEF++ + A A+
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----------FAFVEFEEAESAAKAI 55
Query: 203 DALHGYKFDDK 213
+ +HG F ++
Sbjct: 56 EEVHGKSFANQ 66
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 11/82 (13%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
++V LP D +++ +F Y IR I + RR G FVEF+DP+ A A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVF---YKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDAV 78
Query: 203 DALHGYKFDDKKPDSPTLKIQF 224
GY +D + L+++F
Sbjct: 79 YGRDGYDYDGYR-----LRVEF 95
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 10/95 (10%)
Query: 131 AGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRV-IHKEPRRTGDRAMVLCF 189
AGS + E LF+ LP + +++ +F PF +V I K+ + + F
Sbjct: 16 AGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT----NLSKCFGF 71
Query: 190 VEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQF 224
V +D+P A+ A+ +++G++ K+ LK+Q
Sbjct: 72 VSYDNPVSAQAAIQSMNGFQIGMKR-----LKVQL 101
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 10/82 (12%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRV-IHKEPRRTGDRAMVLCFVEFDDPKCARTA 201
LF+ LP + T +++ F PF +V I K+ + FV FD+P A+ A
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLS----KCFGFVSFDNPDSAQVA 98
Query: 202 MDALHGYKFDDKKPDSPTLKIQ 223
+ A++G++ K+ LK+Q
Sbjct: 99 IKAMNGFQVGTKR-----LKVQ 115
>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 = 35.0 bits (79), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 134 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE-PRRTGDRAMVLCFVEF 192
P + E +LFV G+ + T ++ F Y EI+ IH RRTG VE+
Sbjct: 17 PQRSVEGWILFVTGVHEEATEEDIHD---KFAEYGEIKNIHLNLDRRTG-YLKGYTLVEY 72
Query: 193 DDPKCARTAMDALHG 207
+ K A+ AM+ L+G
Sbjct: 73 ETYKEAQAAMEGLNG 87
>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 = 35.0 bits (79), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 134 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE-PRRTGDRAMVLCFVEF 192
P + E +LFV G+ + T ++ F Y EI+ IH RRTG VE+
Sbjct: 16 PQRSVEGWILFVTGVHEEATEEDIHD---KFAEYGEIKNIHLNLDRRTG-YLKGYTLVEY 71
Query: 193 DDPKCARTAMDALHG 207
+ K A+ AM+ L+G
Sbjct: 72 ETYKEAQAAMEGLNG 86
>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 = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 134 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFD 193
P + E +LFV G+ + T ++ F Y EI+ IH R VE++
Sbjct: 3 PQRSVEGWILFVTGVHEEATEEDIHD---KFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 59
Query: 194 DPKCARTAMDALHG 207
K A+ AM+ L+G
Sbjct: 60 TYKEAQAAMEGLNG 73
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 134 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE-PRRTGDRAMVLCFVEF 192
P + E +LFV G+ + T ++ F Y EI+ IH RRTG VE+
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHD---KFAEYGEIKNIHLNLDRRTG-YLKGYTLVEY 56
Query: 193 DDPKCARTAMDALHG 207
+ K A+ AM+ L+G
Sbjct: 57 ETYKEAQAAMEGLNG 71
>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 = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 134 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFD 193
P + E +LFV G+ + T ++ F Y EI+ IH R VE++
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHD---KFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 57
Query: 194 DPKCARTAMDALHG 207
K A+ AM+ L+G
Sbjct: 58 TYKEAQAAMEGLNG 71
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 139 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 198
E + LF+ GLP CT+ E+ + + +++R++ R G + L +VE+++ A
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLV---TNRAG-KPKGLAYVEYENESQA 71
Query: 199 RTAMDALHGYKFDD 212
A+ + G +
Sbjct: 72 SQAVMKMDGMTIKE 85
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 34.7 bits (78), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
LFV GL D + + +F + E+ V+ R R+ FV F++ A+ AM
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKD---RETQRSRGFGFVTFENIDDAKDAM 71
Query: 203 DALHGYKFDDKK 214
A++G D ++
Sbjct: 72 MAMNGKSVDGRQ 83
>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 = 34.7 bits (78), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 134 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE-PRRTGDRAMVLCFVEF 192
P + E +LFV G+ + T ++ F Y EI+ IH RRTG VE+
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIH---DKFAEYGEIKNIHLNLDRRTG-YLKGYTLVEY 56
Query: 193 DDPKCARTAMDALHG 207
+ K A+ AM+ L+G
Sbjct: 57 ETYKEAQAAMEGLNG 71
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 33.9 bits (76), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 140 SNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCAR 199
S+ L+V L + T + +F PF I V+ K+ TG R+ F+ F D +CAR
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNI-VLMKDSD-TG-RSKGYGFITFSDSECAR 61
Query: 200 TAMDALHGYKF 210
A++ L+G++
Sbjct: 62 RALEQLNGFEL 72
>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 = 33.9 bits (76), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
L V+ LP + T+ E LF +++ + TG +++ FV + DPK A A+
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVR--DKITG-QSLGYGFVNYIDPKDAEKAI 61
Query: 203 DALHGYKFDDKKPDSPTLKIQFAH 226
+ L+G + K T+K+ +A
Sbjct: 62 NTLNGLRLQTK-----TIKVSYAR 80
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 33.9 bits (76), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
L V+ LP + T+ E LF +++ + TG +++ FV + DP A A+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVR--DKITG-QSLGYGFVNYSDPNDADKAI 63
Query: 203 DALHGYKFDDKKPDSPTLKIQFAH 226
+ L+G K K T+K+ +A
Sbjct: 64 NTLNGLKLQTK-----TIKVSYAR 82
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 33.9 bits (76), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 9/86 (10%)
Query: 125 SSLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRA 184
++L+ + P++ L+V L + T + +F PF I+++ TG R+
Sbjct: 17 NNLQKGSAGPMR------LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE--TG-RS 67
Query: 185 MVLCFVEFDDPKCARTAMDALHGYKF 210
F+ F D +CA+ A++ L+G++
Sbjct: 68 KGYGFITFSDSECAKKALEQLNGFEL 93
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
L V+ LP + T+ E LF +++ + TG +++ FV + DP A A+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVR--DKITG-QSLGYGFVNYSDPNDADKAI 63
Query: 203 DALHGYKFDDKKPDSPTLKIQFAH 226
+ L+G K K T+K+ +A
Sbjct: 64 NTLNGLKLQTK-----TIKVSYAR 82
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 19/84 (22%)
Query: 139 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL----------- 187
++N +FV GL + T V+ F+ +I +I K ++TG + L
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFK------QIGII-KTNKKTGQPMINLYTDRETGKLKG 64
Query: 188 -CFVEFDDPKCARTAMDALHGYKF 210
V FDDP A+ A+D G +F
Sbjct: 65 EATVSFDDPPSAKAAIDWFDGKEF 88
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 11/68 (16%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
LF+ LP + T +E+ LF + E +I + G FV +D A A+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII----KNYG-------FVHIEDKTAAEDAI 59
Query: 203 DALHGYKF 210
LH YK
Sbjct: 60 RNLHHYKL 67
>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 = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
+FV +P + +++ LF + EI V+ ++ + ++ CFV F K A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVL-RDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 203 DALHGYK 209
+ALH K
Sbjct: 65 NALHNMK 71
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 19/84 (22%)
Query: 139 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVL----------- 187
++N +FV GL + T V+ F+ +I +I K ++TG + L
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFK------QIGII-KTNKKTGQPMINLYTDRETGKLKG 58
Query: 188 -CFVEFDDPKCARTAMDALHGYKF 210
V FDDP A+ A+D G +F
Sbjct: 59 EATVSFDDPPSAKAAIDWFDGKEF 82
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE----PRRTGDRAMVLCFVEFDDPKCA 198
+FV +P + +++ LF + EI V+ P+ G CFV F K A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG-----CCFVTFYTRKAA 72
Query: 199 RTAMDALHGYK 209
A +ALH K
Sbjct: 73 LEAQNALHNMK 83
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 12/82 (14%)
Query: 126 SLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAM 185
S +NNA E LF+ + CT ++ +F F E R++ R D
Sbjct: 99 SEKNNAV------EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRIL-----RGPDGLS 147
Query: 186 VLC-FVEFDDPKCARTAMDALH 206
C FV F A+TA+ A+H
Sbjct: 148 RGCAFVTFTTRAMAQTAIKAMH 169
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE----PRRTGDRAMVLCFVEFDDPKCA 198
+FV +P + +++ LF + EI V+ P+ G CFV F K A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG-----CCFVTFYTRKAA 60
Query: 199 RTAMDALHGYK 209
A +ALH K
Sbjct: 61 LEAQNALHNMK 71
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 12/82 (14%)
Query: 126 SLRNNAGSPLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAM 185
S +NNA E LF+ + CT ++ +F F E R++ R D
Sbjct: 87 SEKNNAV------EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRIL-----RGPDGLS 135
Query: 186 VLC-FVEFDDPKCARTAMDALH 206
C FV F A+TA+ A+H
Sbjct: 136 RGCAFVTFTTRAMAQTAIKAMH 157
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 141 NLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCART 200
N +FV G+P +C E+ F+ F E+ +I+ ++ R F+ F+D +
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQ---RPRGFGFITFEDEQSVDQ 67
Query: 201 AMD 203
A++
Sbjct: 68 AVN 70
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 31.2 bits (69), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
L++ GLP T+++V +F F RV+ + T + + F+ FD A A+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ---TTGLSRGVAFIRFDKRSEAEEAI 147
Query: 203 DALHGYK 209
+ +G+K
Sbjct: 148 TSFNGHK 154
>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 = 30.8 bits (68), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
L++ GLP T+++V +F F RV+ + T + + F+ FD A A+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ---TTGLSRGVAFIRFDKRSEAEEAI 147
Query: 203 DALHGYK 209
+ +G+K
Sbjct: 148 TSFNGHK 154
>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 = 30.8 bits (68), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 144 FVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMD 203
FV +P + +++ LF + EI V+ ++ + ++ CFV F K A A +
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVL-RDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 204 ALHGYK 209
ALH K
Sbjct: 66 ALHNXK 71
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.4 bits (67), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
L V+ LP D T RE+ LFR R++ +TG + FV+F ++ A+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY--KTG-YSYGYAFVDFTSEMDSQRAI 62
Query: 203 DALHGYKFDDKKPDSPTLKIQFAH 226
L+G +K+ LK+ +A
Sbjct: 63 KVLNGITVRNKR-----LKVSYAR 81
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 30.4 bits (67), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 134 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE-PRRTGDRAMVLCFVEF 192
P + E +LFV + + E+ F Y EI+ IH RRTG + VE+
Sbjct: 20 PQRSVEGWILFVTSIHEEAQEDEIQ---EKFCDYGEIKNIHLNLDRRTG-FSKGYALVEY 75
Query: 193 DDPKCARTAMDALHG 207
+ K A A +AL+G
Sbjct: 76 ETHKQALAAKEALNG 90
>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 = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 134 PLKKGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKE-PRRTGDRAMVLCFVEF 192
P + E +LFV + + E+ F Y EI+ IH RRTG + VE+
Sbjct: 66 PQRSVEGWILFVTSIHEEAQEDEIQE---KFCDYGEIKNIHLNLDRRTG-FSKGYALVEY 121
Query: 193 DDPKCARTAMDALHG 207
+ K A A +AL+G
Sbjct: 122 ETHKQALAAKEALNG 136
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAM 202
L V+ LP D T RE+ LFR R++ +TG + FV+F ++ A+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY--KTG-YSYGYAFVDFTSEMDSQRAI 62
Query: 203 DALHGYKFDDKKPDSPTLKIQFAH 226
L+G +K+ LK+ +A
Sbjct: 63 KVLNGITVRNKR-----LKVSYAR 81
>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 = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 160 LFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCARTAMDALHGYKFDDKKPDSPT 219
L R F Y + ++ R + FV F D + A AMDA+ G D ++
Sbjct: 64 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE----- 118
Query: 220 LKIQFAHF 227
L++Q A +
Sbjct: 119 LRVQMARY 126
>pdb|3A9R|A Chain A, X-Ray Structures Of Bacillus Pallidus D-Arabinose
Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
pdb|3A9R|B Chain B, X-Ray Structures Of Bacillus Pallidus D-Arabinose
Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
pdb|3A9R|C Chain C, X-Ray Structures Of Bacillus Pallidus D-Arabinose
Isomerasecomplex With (4r)-2-Methylpentane-2,4-Diol
pdb|3A9S|A Chain A, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With Glycerol
pdb|3A9S|B Chain B, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With Glycerol
pdb|3A9S|C Chain C, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With Glycerol
pdb|3A9T|A Chain A, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With L-Fucitol
pdb|3A9T|B Chain B, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With L-Fucitol
pdb|3A9T|C Chain C, X-Ray Structure Of Bacillus Pallidus D-Arabinose Isomerase
Complex With L-Fucitol
Length = 595
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 98 DPNLIGQRRDIAPGINPTIPDVINGVPSSLR----NNAGSPLKKGESNLLFVDGLPTDCT 153
DP +G I GI PTI GV SL N A + K E N+ + +G P +C
Sbjct: 4 DPRYVGNLPKI--GIRPTIDGRRKGVRESLEETTMNMAKAVAKLLEENVFYYNGQPVECV 61
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 143 LFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC-FVEFDDPKCARTA 201
LFV L + +V LF+PF E V+ R D + C FV+F A+ A
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVL-----RGPDGSSKGCAFVKFSSHTEAQAA 72
Query: 202 MDALHGYK 209
+ ALHG +
Sbjct: 73 IHALHGSQ 80
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 142 LLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHK-EPRRTGDRAMVLCFVEFDDPKCART 200
+L++ LP T E+ +F + R+IRV + E R T +V ++D A+
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGT-------AYVVYEDIFDAKN 62
Query: 201 AMDALHGYKFDDK 213
A+D L G+ ++
Sbjct: 63 AVDHLSGFNVSNR 75
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 139 ESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLCFVEFDDPKCA 198
E LFV GL T+ + F + G VI K+ +T +++ FV+F DP C
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQY-GEVVDCVIMKD--KTTNQSRGFGFVKFKDPNCV 71
Query: 199 RTAM 202
T +
Sbjct: 72 GTVL 75
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 137 KGESNLLFVDGLPTDCTRREVSHLFRPFVGYREIRVIHKEPRRTGDRAMVLC-FVEFDDP 195
+GE LFV L T +V +F PF E V+ R D C FV+F
Sbjct: 9 RGEDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVL-----RGPDGTSKGCAFVKFQTH 63
Query: 196 KCARTAMDALH 206
A+ A++ LH
Sbjct: 64 AEAQAAINTLH 74
>pdb|2WHW|A Chain A, Selective Oxidation Of Carbolide C-H Bonds By Engineered
Macrolide P450 Monooxygenase
pdb|2WHW|B Chain B, Selective Oxidation Of Carbolide C-H Bonds By Engineered
Macrolide P450 Monooxygenase
pdb|2WI9|A Chain A, Selective Oxidation Of Carbolide C-H Bonds By Engineered
Macrolide P450 Monooxygenase
pdb|2WI9|B Chain B, Selective Oxidation Of Carbolide C-H Bonds By Engineered
Macrolide P450 Monooxygenase
Length = 436
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 176 EPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY 208
EP R R FV DDP A+TAM + GY
Sbjct: 185 EPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGY 217
>pdb|2BVJ|A Chain A, Ligand-Free Structure Of Cytochrome P450 Pikc (Cyp107l1)
pdb|2BVJ|B Chain B, Ligand-Free Structure Of Cytochrome P450 Pikc (Cyp107l1)
pdb|2C6H|A Chain A, Crystal Structure Of Yc-17-Bound Cytochrome P450 Pikc
(Cyp107l1)
pdb|2C6H|B Chain B, Crystal Structure Of Yc-17-Bound Cytochrome P450 Pikc
(Cyp107l1)
pdb|2C7X|A Chain A, Crystal Structure Of Narbomycin-Bound Cytochrome P450 Pikc
(Cyp107l1)
pdb|2CA0|A Chain A, Crystal Structure Of Yc-17-Bound Cytochrome P450 Pikc
(Cyp107l1)
pdb|2CA0|B Chain B, Crystal Structure Of Yc-17-Bound Cytochrome P450 Pikc
(Cyp107l1)
pdb|2CD8|A Chain A, Crystal Structure Of Yc-17-Bound Cytochrome P450 Pikc
(Cyp107l1)
pdb|2CD8|B Chain B, Crystal Structure Of Yc-17-Bound Cytochrome P450 Pikc
(Cyp107l1)
Length = 436
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 176 EPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY 208
EP R R FV DDP A+TAM + GY
Sbjct: 185 EPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGY 217
>pdb|2VZ7|A Chain A, Crystal Structure Of The Yc-17-Bound Pikc D50n Mutant
pdb|2VZ7|B Chain B, Crystal Structure Of The Yc-17-Bound Pikc D50n Mutant
pdb|2VZM|A Chain A, Crystal Structure Of The Narbomycin-Bound Pikc D50n Mutant
pdb|2VZM|B Chain B, Crystal Structure Of The Narbomycin-Bound Pikc D50n Mutant
Length = 436
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 176 EPRRTGDRAMVLCFVEFDDPKCARTAMDALHGY 208
EP R R FV DDP A+TAM + GY
Sbjct: 185 EPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGY 217
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 187 LCFVEFDDPKCARTAMDALHGYKFDDKKPDSPTLKIQFAHF 227
FV F D + A AMDA+ G D ++ L++Q A +
Sbjct: 114 FAFVRFHDKRDAEDAMDAMDGAVLDGRE-----LRVQMARY 149
>pdb|1Y8Q|A Chain A, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8Q|C Chain C, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8R|A Chain A, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
pdb|1Y8R|D Chain D, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
pdb|3KYC|A Chain A, Human Sumo E1 Complex With A Sumo1-Amp Mimic
pdb|3KYD|A Chain A, Human Sumo E1~sumo1-amp Tetrahedral Intermediate Mimic
Length = 346
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 44 GFRGASDFLHREVTPMRPGALGLVDTAGVG 73
G +G + H +VTP PGA L+ T VG
Sbjct: 59 GVKGLTMLDHEQVTPEDPGAQFLIRTGSVG 88
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.138 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,185,817
Number of Sequences: 62578
Number of extensions: 353329
Number of successful extensions: 728
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 38
Number of HSP's that attempted gapping in prelim test: 704
Number of HSP's gapped (non-prelim): 55
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)