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= psy11527
(206 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 7/85 (8%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAI 157
G +GM+ LFV NL V+E+ ++ F F RV+ AFI + + + A+
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK----DYAFIHFDERDGAV 59
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAK 182
+AM +NG L + I I +AK
Sbjct: 60 KAMEEMNGKDLEGEN---IEIVFAK 81
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 108 LFVANLGQFVSEQEIKDI---FGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNL 163
LF+ L ++++ ++K++ FG F+ V+ G S AF EY D+N QA++ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 164 NGSYLASS 171
NG L
Sbjct: 64 NGMQLGDK 71
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 108 LFVANLGQFVSEQEIKDI---FGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNL 163
LF+ L ++++ ++K++ FG F+ V+ G S AF EY D+N QA++ L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 164 NGSYLASS 171
NG L
Sbjct: 177 NGMQLGDK 184
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 108 LFVANLGQFVSEQEIKDI---FGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNL 163
LF+ L ++++ ++K++ FG F+ V+ G S AF EY D+N QA++ L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 164 NGSYLASS 171
NG L
Sbjct: 159 NGMQLGDK 166
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 7/82 (8%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSF-PGFS-RVRMHNKGGSP--VAFIEYTDVNFAIQAMSN 162
++FV N+ +E+++KDIF P S R+ + G P F EY D A+ AM N
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 163 LNGSYLASSDRGAIRIEYAKTK 184
LNG + A+R++ A ++
Sbjct: 70 LNGREFSGR---ALRVDNAASE 88
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 108 LFVANLGQFVSEQEIKDI---FGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNL 163
LF+ L ++++ ++K++ FG F+ V+ G S AF EY D+N QA++ L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 164 NGSYLASS 171
NG L
Sbjct: 157 NGMQLGDK 164
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGS--FPGFSRVRMHNKGGSPVAFIEYTDVNF 155
G +G S + L++ NL V+ +++ +FG P +V + S AF++Y D N+
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK----SGYAFVDYPDQNW 56
Query: 156 AIQAMSNLNG 165
AI+A+ L+G
Sbjct: 57 AIRAIETLSG 66
>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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 97 QGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFA 156
Q ++ P LF+ NL + +E + +F FPGF VR+ G +AF+E+ + A
Sbjct: 199 QPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV-PGRHDIAFVEFDNEVQA 257
Query: 157 IQAMSNLNGSYLASSDRGAIRIEYAK 182
A L G + ++ A++I +AK
Sbjct: 258 GAARDALQGFKITQNN--AMKISFAK 281
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 97 QGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFA 156
Q ++ P LF+ NL + +E + +F FPGF VR+ G +AF+E+ + A
Sbjct: 5 QPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV-PGRHDIAFVEFDNEVQA 63
Query: 157 IQAMSNLNGSYLASSDRGAIRIEYAK 182
A L G + ++ A++I +AK
Sbjct: 64 GAARDALQGFKITQNN--AMKISFAK 87
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMS 161
M+ LFV NL V+E+ ++ F F RV+ AF+ + D A++AM
Sbjct: 12 MAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLK----DYAFVHFEDRGAAVKAMD 67
Query: 162 NLNG 165
+NG
Sbjct: 68 EMNG 71
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 97 QGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-KGGSPVAFIEYTDVNF 155
+G G + C ++V NL + ++I+D+F + + + N +GG P AF+E+ D
Sbjct: 15 RGPAGNNDCR-IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRD 73
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAKT 183
A A+ +G D +R+E+ ++
Sbjct: 74 AEDAVYGRDG---YDYDGYRLRVEFPRS 98
>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 = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
P LF+ NL + +E + +F FPGF VR+ +AF+E+T + A L
Sbjct: 7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLV-PNRHDIAFVEFTTELQSNAAKEAL 65
Query: 164 NGSYLASSDRGAIRIEYAK 182
G + + A++I +AK
Sbjct: 66 QGFKITPTH--AMKITFAK 82
>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 = 0.066, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSR---VRMHNKGGS-PVAFIEYTDVNFAI 157
M + L V L Q +++ E K +FGS VR G S F+ Y+D N A
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAK 182
+A++ LNG L + I++ YA+
Sbjct: 61 KAINTLNGLKLQTK---TIKVSYAR 82
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 33.9 bits (76), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSR---VRMHNKGGS-PVAFIEYTDVNFAI 157
M + L V L Q +++ E K +FGS VR G S F+ Y+D N A
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAK 182
+A++ LNG L + I++ YA+
Sbjct: 61 KAINTLNGLKLQTK---TIKVSYAR 82
>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 = 0.14, Method: Compositional matrix adjust.
Identities = 33/102 (32%), Positives = 50/102 (49%), Gaps = 8/102 (7%)
Query: 106 STLFVANLG-QFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSNL 163
S L V+NL + V+ Q + +FG + RV+ + NK + A ++ D N A AMS+L
Sbjct: 35 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN--ALVQMADGNQAQLAMSHL 92
Query: 164 NGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQGTK-YGYT 204
NG L IRI +K + + E + TK YG +
Sbjct: 93 NGHKLHGK---PIRITLSKHQNVQLPREGQEDQGLTKDYGNS 131
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 33/102 (32%), Positives = 50/102 (49%), Gaps = 8/102 (7%)
Query: 106 STLFVANLG-QFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSNL 163
S L V+NL + V+ Q + +FG + RV+ + NK + A ++ D N A AMS+L
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN--ALVQMADGNQAQLAMSHL 61
Query: 164 NGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQGTK-YGYT 204
NG L IRI +K + + E + TK YG +
Sbjct: 62 NGHKLHGK---PIRITLSKHQNVQLPREGQEDQGLTKDYGNS 100
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
+ LFV V E E+ +IFG F V++ N AF+E+ + A +A+ ++G
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG----FAFVEFEEAESAAKAIEEVHG 87
Query: 166 SYLASS 171
A+
Sbjct: 88 KSFANQ 93
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 30.8 bits (68), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSF-PG-FSRVRMHNKGGSPVAFIEYTDVNFAIQA 159
MS L+V NL SE+ I+ F + PG RV+ AF+ +++ A++A
Sbjct: 12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD----YAFVHFSNREDAVEA 67
Query: 160 MSNLNGSYLASS 171
M LNG L S
Sbjct: 68 MKALNGKVLDGS 79
>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 = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGF--SRVRMHNKGGSP--VAFIEYTDVNFAIQAMS 161
+ L+V NL + +++ ++ IFG + + G P VAF+ Y A +A+S
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 162 NLN 164
LN
Sbjct: 74 ALN 76
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
+ LFV V E E+ +IFG F V++ N AF+E+ + A +A+ ++G
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG----FAFVEFEEAESAAKAIEEVHG 60
Query: 166 SYLAS 170
A+
Sbjct: 61 KSFAN 65
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSR--VRMHNKGGSP--VAFIEYTDVNFAIQAMS 161
+ L+V NL + +++ ++ IFG + + + G P VAF+ Y A +A+S
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 162 NLN 164
LN
Sbjct: 150 ALN 152
>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 = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGF--SRVRMHNKGGSP--VAFIEYTDVNFAIQAMS 161
+ L+V NL + +++ ++ IFG + + G P VAF+ Y A +A+S
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 162 NLN 164
LN
Sbjct: 161 ALN 163
>pdb|3BIF|A Chain A, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase Empty
6-Pf-2k Active Site
Length = 468
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDI 125
G G+SP F +L QF+S+Q IKD+
Sbjct: 269 GDPGLSPRGREFSKHLAQFISDQNIKDL 296
>pdb|1BIF|A Chain A, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase
Bifunctional Enzyme Complexed With Atp-G-S And Phosphate
Length = 469
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDI 125
G+SP F +L QF+S+Q IKD+
Sbjct: 273 GLSPRGREFSKHLAQFISDQNIKDL 297
>pdb|2BIF|A Chain A, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase H256a
Mutant With F6p In Phosphatase Active Site
pdb|2BIF|B Chain B, 6-Phosphofructo-2-KinaseFRUCTOSE-2,6-Bisphosphatase H256a
Mutant With F6p In Phosphatase Active Site
Length = 469
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDI 125
G+SP F +L QF+S+Q IKD+
Sbjct: 273 GLSPRGREFSKHLAQFISDQNIKDL 297
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP---VAFIEYTDVNFAIQAMSNLN 164
LF+ L + +E+ +K +FG S V + S AFI + + A A ++N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 165 GSYLASSDRGAIRIEYAK 182
G L AI++E AK
Sbjct: 70 GKSLHGK---AIKVEQAK 84
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAI 157
M G SP + V NL V+ + IF F ++ K A ++Y D A
Sbjct: 26 AMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 85
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAK 182
A +L+G + ++ +RI+++K
Sbjct: 86 HAKLSLDGQNIYNA-CCTLRIDFSK 109
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVR---MHNKGGSP--VAFIEYTDVNFAIQAM 160
ST+FVANL V +++K++F S G VR + +K G + + + A+QA+
Sbjct: 16 STVFVANLDYKVGWKKLKEVF-SMAGVV-VRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
Query: 161 SNLNGSYL 168
S NG L
Sbjct: 74 SMFNGQLL 81
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 8/89 (8%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSR----VRMHNKGGSP-VAFIEYTDVNF 155
G S S +F+ NL + E+ + D F +F + +R + G S AFI + +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ A+ +NG YL + I + YA K
Sbjct: 61 SDAAIEAMNGQYLCNR---PITVSYAFKK 86
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/65 (21%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAIQAMSNLNG 165
L+V NL + ++ ++ F F + ++ +GG F+ ++ A +A++ +NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 166 SYLAS 170
+A+
Sbjct: 78 RIVAT 82
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAI 157
M G SP + V NL V+ + IF F ++ K A ++Y D A
Sbjct: 21 AMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 80
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAK 182
A +L+G + ++ +RI+++K
Sbjct: 81 HAKLSLDGQNIYNA-CCTLRIDFSK 104
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAI 157
G +G S LF+ NL + +EQEI+ +F + + G F+ D A
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYG----FVHIEDKTAAE 56
Query: 158 QAMSNL 163
A+ NL
Sbjct: 57 DAIRNL 62
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 27.3 bits (59), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGF--SRVRMHNKGGSP--VAFIEYTDVNFAIQAMSN 162
LFV +L V ++ +++ F FP + V + GS F+ +T + A AM +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 163 LNGSYLASSDRGAIRIEYA 181
+ G L +RI +A
Sbjct: 63 MQGQDLNGR---PLRINWA 78
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 27.3 bits (59), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSNLNG 165
TL ++NL +E+ ++++F F +V + G S AFIE+ A +A+++ N
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK-ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNK 75
Query: 166 SYLASSDRGAIRIE 179
+ AIR+E
Sbjct: 76 REIEGR---AIRLE 86
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAI 157
M G SP + V NL V+ + IF F ++ K A ++Y D A
Sbjct: 39 AMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 98
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAK 182
A +L+G + ++ +RI+++K
Sbjct: 99 HAKLSLDGQNIYNA-CCTLRIDFSK 122
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 26.6 bits (57), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 98 GMNGMSPC-------STLFVANLGQFVSEQEIKDIFGSFPGFSR---VRMHNKGGSPVAF 147
G +G S C LFV L + SE +++ +F +F +R + AF
Sbjct: 1 GSSGSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAF 60
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKT 183
++Y+ A A++ L+GS ++ +++A T
Sbjct: 61 VKYSSHAEAQAAINALHGSQTMPGASSSLVVKFADT 96
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
0.320 0.133 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,166,656
Number of Sequences: 62578
Number of extensions: 223843
Number of successful extensions: 543
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 30
Number of HSP's that attempted gapping in prelim test: 520
Number of HSP's gapped (non-prelim): 48
length of query: 206
length of database: 14,973,337
effective HSP length: 94
effective length of query: 112
effective length of database: 9,091,005
effective search space: 1018192560
effective search space used: 1018192560
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)