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= 024424
(268 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/33 (66%), Positives = 25/33 (75%)
Query: 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
FAFVEF DPRDA+DA Y +G D DG R+ VEF
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 95
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/34 (58%), Positives = 26/34 (76%)
Query: 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
FAFVEF DPRDA+DA L+G+ + GSR+ VE +
Sbjct: 39 FAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 72
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/34 (58%), Positives = 24/34 (70%)
Query: 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
FAFVEF DPRDA DA L+GR + G R+ VE +
Sbjct: 112 FAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/34 (58%), Positives = 24/34 (70%)
Query: 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
FAFVEF DPRDA DA L+GR + G R+ VE +
Sbjct: 112 FAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELS 145
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
RD+AFV FS+ DA +A +LNG+ +DGS I V A
Sbjct: 51 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In
Complex With An Inhibitor Displaying A 2 Inhibitors:1
Nc Stoichiometry
Length = 55
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
+CFNCG +GH A++C+A K C++CG+ GH ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KKGCWKCGKEGHQMKDC 49
Score = 27.7 bits (60), Expect = 7.8, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 84 KCYRCGERGHIERNCQNSPKK 104
KC+ CG+ GHI +NC+ KK
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKK 34
>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The
Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses
In The Binding Polarity Of Nc
Length = 45
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
+CFNCG +GH AR+C+A K C++CG+ GH ++C
Sbjct: 4 KCFNCGKEGHTARNCRAPR-KKGCWKCGKEGHQMKDC 39
>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To
Stem-Loop Sl2 Of The Psi-Rna Packaging Signal.
Implications For Genome Recognition
Length = 56
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
+CFNCG +GH A++C+A K C++CG+ GH ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KKGCWKCGKEGHQMKDC 49
Score = 27.3 bits (59), Expect = 8.1, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 84 KCYRCGERGHIERNCQNSPKK 104
KC+ CG+ GHI +NC+ KK
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKK 34
>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid
(Ncp7(12-55)) Complexed With The Dna (-) Primer Binding
Site
pdb|2JZW|A Chain A, How The Hiv-1 Nucleocapsid Protein Binds And
Destabilises The (-)primer Binding Site During Reverse
Transcription
Length = 44
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
+CFNCG +GH AR+C+A K C++CG+ GH ++C
Sbjct: 3 KCFNCGKEGHTARNCRAPR-KKGCWKCGKEGHQMKDC 38
>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES
pdb|1ESK|A Chain A, Solution Structure Of Ncp7 From Hiv-1
Length = 42
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
+CFNCG +GH AR+C+A K C++CG+ GH ++C
Sbjct: 3 KCFNCGKEGHTARNCRAPR-KKGCWKCGKEGHQMKDC 38
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus
Type-2 Nucleocapsid Protein
Length = 49
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
RC+NCG +GH AR C+A + C++CG+ GH+ C
Sbjct: 8 RCWNCGKEGHSARQCRAPR-RQGCWKCGKTGHVMAKC 43
>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The
Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures
pdb|1MFS|A Chain A, Dynamical Behavior Of The Hiv-1 Nucleocapsid Protein;
Nmr, 30 Structures
Length = 55
Score = 37.7 bits (86), Expect = 0.007, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
+CFNCG +GH A++C+A K C++CG+ GH ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KKGCWKCGKEGHQMKDC 49
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses:
Exafs Studies On Intact Viruses And The Solution-State
Structure Of The Nucleocapsid Protein From Hiv-1
Length = 55
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
+CFNCG +GH A++C+A K C++CG+ GH ++C
Sbjct: 14 KCFNCGKEGHIAKNCRAPR-KRGCWKCGKEGHQMKDC 49
>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 = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
R FAFV F D RDA+DA +++G +DG + V+ A
Sbjct: 89 RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
R FAF+ F +P DA +A +NG+ + G I VE A
Sbjct: 48 RGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
R FAFV F D RDA DA +++G ++DG + V+ A
Sbjct: 55 RGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA 90
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 35.4 bits (80), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 22/38 (57%)
Query: 1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
+ +D+AFV DA A LNG++V G RI VE +
Sbjct: 41 VVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS 78
>pdb|3TS0|A Chain A, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
pdb|3TS0|B Chain B, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
Length = 146
Score = 35.4 bits (80), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 57 PPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
P G RC+NCG H A++CK KC+ C H+ +C
Sbjct: 92 PKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASC 133
>pdb|3TRZ|A Chain A, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|B Chain B, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|C Chain C, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|D Chain D, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|E Chain E, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|F Chain F, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TS2|A Chain A, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
pdb|3TS2|B Chain B, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
Length = 148
Score = 35.4 bits (80), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 57 PPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
P G RC+NCG H A++CK KC+ C H+ +C
Sbjct: 94 PKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASC 135
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.4 bits (80), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
R FAFV F D RDA+DA +++G +DG + V+ A
Sbjct: 112 RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 34.7 bits (78), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
R F FV F + DA DA ++NG+ VDG +I V+
Sbjct: 54 RGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 34.7 bits (78), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
R FAFV F + DA +A+ NG ++DG RI V+F+
Sbjct: 88 RGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
R FAFV F + DA +A+ NG ++DG RI V+F+
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 92
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
RC+NCG H A++CK KC+ C H+ +C
Sbjct: 26 RCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASC 62
>pdb|1Q3Y|A Chain A, Nmr Structure Of The Cys28his Mutant (D Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1.
pdb|1Q3Z|A Chain A, Nmr Structure Of The Cys28his Mutant (e Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1
Length = 42
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 26/37 (70%), Gaps = 1/37 (2%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
+CFNCG +GH AR+ +A K C++CG+ GH ++C
Sbjct: 3 KCFNCGKEGHTARNHRAPR-KKGCWKCGKEGHQMKDC 38
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
+ FV +SDP DAD A +LNG + I V +A
Sbjct: 48 YGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYA 81
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
R FAFV F + DA +A+ NG ++DG RI V+F+
Sbjct: 54 RGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89
>pdb|2CQF|A Chain A, Solution Structure Of The Zinc-Finger Domain In Lin-28
Length = 63
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 62 RCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNC 98
RC+NCG H A++CK KC+ C H+ +C
Sbjct: 9 RCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASC 45
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 32.3 bits (72), Expect = 0.27, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 63 CFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQN 100
C+NCG GH + C+A C++C + GH + C++
Sbjct: 3 CYNCGKPGHLSSQCRA---PKVCFKCKQPGHFSKQCRS 37
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 32.3 bits (72), Expect = 0.32, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
+ FV +SDP DAD A +LNG + I V +A
Sbjct: 48 YGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYA 81
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
R +AF+E+ RD A +G+ +DG R++V+
Sbjct: 144 RGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 178
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRI 33
+ F FVE+ P A A L G VDG ++
Sbjct: 48 LSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKL 80
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.2 bits (69), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
+D+AF+ F + A A +NG+D++G I + FA
Sbjct: 45 KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA 80
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36
R +AF+E+ RD A +G+ +DG R++V+
Sbjct: 144 RGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 177
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV 35
R FAFV F + DA +A+ NG ++DG RI V
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37
+ +AF+EF+ DA +A S N R+++G I +E
Sbjct: 53 KGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>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 = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
+ FV + DP+DA+ A +LNG + I V +A
Sbjct: 46 YGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.0 bits (66), Expect = 1.3, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRI 33
+ + +A+VEF +P +A+ A ++G +DG I
Sbjct: 45 LSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike
Domain Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 62 RCFNCGIDGHWARDCKA 78
+CFNCG +GH AR+C+A
Sbjct: 2 KCFNCGKEGHIARNCRA 18
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 84 KCYRCGERGHIERNCQ 99
KC+ CG+ GHI RNC+
Sbjct: 2 KCFNCGKEGHIARNCR 17
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRI 33
+ F FV F + DAD AR L+G V+G +I
Sbjct: 69 KGFGFVTFENSADADRAREKLHGTVVEGRKI 99
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 23/35 (65%)
Query: 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
++AFVE+ DA+ A +LNG+ ++ + + + +A
Sbjct: 42 NYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA 76
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRI 33
+ F FV F + DAD AR L+G V+G +I
Sbjct: 55 KGFGFVTFENSADADRAREKLHGTVVEGRKI 85
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus
Nucleocapsid Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 61 GRCFNCGIDGHWARDC----KAGDWKNKCYRCGERGHIERNC 98
G C+ CG GH+ C K+G+ + +C C GH + C
Sbjct: 5 GLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQC 46
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
+ FVEF + RDA A ++NGR + G + V +A
Sbjct: 57 YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA 90
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 24/36 (66%)
Query: 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38
+ F FV+F+ DA A+ ++ ++DG+++ +++A
Sbjct: 54 KGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA 89
>pdb|1NC8|A Chain A, High-Resolution Solution Nmr Structure Of The Minimal
Active Domain Of The Human Immunodeficiency Virus
Type-2 Nucleocapsid Protein, 15 Structures
Length = 29
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 62 RCFNCGIDGHWARDCKA 78
RC+NCG +GH AR C+A
Sbjct: 8 RCWNCGKEGHSARQCRA 24
>pdb|1NCP|N Chain N, Structural Characterization Of A 39 Residue Synthetic
Peptide Containing The Two Zinc Binding Domains From
The Hiv-1 P7 Nucleocapsid Protein By Cd And Nmr
Spectroscopy
Length = 17
Score = 27.7 bits (60), Expect = 6.1, Method: Composition-based stats.
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 62 RCFNCGIDGHWARDCK 77
+CFNCG +GH AR+C+
Sbjct: 2 KCFNCGKEGHTARNCR 17
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
0.314 0.136 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,338,056
Number of Sequences: 62578
Number of extensions: 224905
Number of successful extensions: 482
Number of sequences better than 100.0: 57
Number of HSP's better than 100.0 without gapping: 54
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 380
Number of HSP's gapped (non-prelim): 92
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)