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= psy13906
(914 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 141 bits (355), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 69/155 (44%), Positives = 103/155 (66%), Gaps = 1/155 (0%)
Query: 442 MRHIMQGKEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLI 501
+R +M GKEVGSIIGK GE+VKK+REESG++I IS+ + PERI+T+ G +++F+AF++I
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMI 66
Query: 502 TKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCXXXXXXXXXXXXXXRETSGASVYVA 561
+EE + + + LRL+VPASQC RE++GA V VA
Sbjct: 67 IDKLEEDISSSMTNSTAASRPP-VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVA 125
Query: 562 SDMLPNSTEREVNIKGVPDAVTQAIYQICLIMVDS 596
DMLPNSTER + I G+P ++ + + QIC++M+++
Sbjct: 126 GDMLPNSTERAITIAGIPQSIIECVKQICVVMLET 160
Score = 138 bits (347), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 68/151 (45%), Positives = 100/151 (66%), Gaps = 1/151 (0%)
Query: 1 MQGKEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLITKNI 60
M GKEVGSIIGK GE+VKK+REESG++I IS+ + PERI+T+ G +++F+AF++I +
Sbjct: 11 MHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKL 70
Query: 61 EEFHKNQNKHLGGNGESQLIQLRLIVPASQCXXXXXXXXXXXXXXRETSGASVYVASDML 120
EE + + + LRL+VPASQC RE++GA V VA DML
Sbjct: 71 EEDISSSMTNSTAASRPP-VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDML 129
Query: 121 PNSTEREVNIKGVPDAVTQAIYQICLIMVDS 151
PNSTER + I G+P ++ + + QIC++M+++
Sbjct: 130 PNSTERAITIAGIPQSIIECVKQICVVMLET 160
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 266 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAI 321
+ VP G++IGKGG KI EIR+ +GA +++ +R IT+ G P +I
Sbjct: 93 LVVPASQCGSLIGKGGCKIKEIRESTGAQVQV--AGDMLPNSTERAITIAGIPQSI 146
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 711 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAI 766
+ VP G++IGKGG KI EIR+ +GA +++ +R IT+ G P +I
Sbjct: 93 LVVPASQCGSLIGKGGCKIKEIRESTGAQVQV--AGDMLPNSTERAITIAGIPQSI 146
>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|B Chain B, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|C Chain C, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|D Chain D, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
Length = 76
Score = 81.3 bits (199), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 36/66 (54%), Positives = 55/66 (83%)
Query: 442 MRHIMQGKEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLI 501
+R +M GKEVGSIIGK GE+VK++REESG++I IS+ ++PERI+T+ G +++F+AF++I
Sbjct: 5 IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNSPERIITLTGPTNAIFKAFAMI 64
Query: 502 TKNIEE 507
+EE
Sbjct: 65 IDKLEE 70
Score = 79.3 bits (194), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 35/62 (56%), Positives = 52/62 (83%)
Query: 1 MQGKEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLITKNI 60
M GKEVGSIIGK GE+VK++REESG++I IS+ ++PERI+T+ G +++F+AF++I +
Sbjct: 9 MHGKEVGSIIGKKGESVKRIREESGARINISEGNSPERIITLTGPTNAIFKAFAMIIDKL 68
Query: 61 EE 62
EE
Sbjct: 69 EE 70
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 273 IGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALAQYLI 328
+G++IGK G + IR+ SGA I I +R IT+TG +AI A +I
Sbjct: 14 VGSIIGKKGESVKRIREESGARINISEGNSP-----ERIITLTGPTNAIFKAFAMI 64
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 718 IGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALAQYLI 773
+G++IGK G + IR+ SGA I I +R IT+TG +AI A +I
Sbjct: 14 VGSIIGKKGESVKRIREESGARINISEGNSP-----ERIITLTGPTNAIFKAFAMI 64
>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|B Chain B, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|C Chain C, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|D Chain D, Human Alpha Polyc Binding Protein Kh1
Length = 74
Score = 81.3 bits (199), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 36/66 (54%), Positives = 54/66 (81%)
Query: 442 MRHIMQGKEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLI 501
+R +M GKEVGSIIGK GE+VK++REESG++I IS+ + PERI+T+ G +++F+AF++I
Sbjct: 5 IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMI 64
Query: 502 TKNIEE 507
+EE
Sbjct: 65 IDKLEE 70
Score = 78.6 bits (192), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 35/62 (56%), Positives = 51/62 (82%)
Query: 1 MQGKEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLITKNI 60
M GKEVGSIIGK GE+VK++REESG++I IS+ + PERI+T+ G +++F+AF++I +
Sbjct: 9 MHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFAMIIDKL 68
Query: 61 EE 62
EE
Sbjct: 69 EE 70
>pdb|2AXY|A Chain A, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|B Chain B, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|C Chain C, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|D Chain D, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2PQU|A Chain A, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|B Chain B, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|C Chain C, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|D Chain D, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PY9|A Chain A, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|B Chain B, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|C Chain C, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|D Chain D, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
Length = 73
Score = 75.1 bits (183), Expect = 2e-13, Method: Composition-based stats.
Identities = 36/66 (54%), Positives = 51/66 (77%)
Query: 442 MRHIMQGKEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLI 501
+R + GKEVGSIIGK GE+VKK REESG++I IS+ + PERI+T+ G +++F+AF+ I
Sbjct: 7 IRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGNCPERIITLAGPTNAIFKAFAXI 66
Query: 502 TKNIEE 507
+EE
Sbjct: 67 IDKLEE 72
Score = 73.6 bits (179), Expect = 5e-13, Method: Composition-based stats.
Identities = 35/61 (57%), Positives = 48/61 (78%)
Query: 2 QGKEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLITKNIE 61
GKEVGSIIGK GE+VKK REESG++I IS+ + PERI+T+ G +++F+AF+ I +E
Sbjct: 12 HGKEVGSIIGKKGESVKKXREESGARINISEGNCPERIITLAGPTNAIFKAFAXIIDKLE 71
Query: 62 E 62
E
Sbjct: 72 E 72
>pdb|2P2R|A Chain A, Crystal Structure Of The Third Kh Domain Of Human Poly(C)-
Binding Protein-2 In Complex With C-Rich Strand Of Human
Telomeric Dna
Length = 76
Score = 66.2 bits (160), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 33/66 (50%), Positives = 46/66 (69%), Gaps = 3/66 (4%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
E+T+PN+LIG +IG+ G KI EIR+ SGA I+I DR +T+TG+ +I+LA
Sbjct: 8 ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKI---ANPVEGSTDRQVTITGSAASISLA 64
Query: 325 QYLINM 330
QYLIN+
Sbjct: 65 QYLINV 70
Score = 66.2 bits (160), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 33/66 (50%), Positives = 46/66 (69%), Gaps = 3/66 (4%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
E+T+PN+LIG +IG+ G KI EIR+ SGA I+I DR +T+TG+ +I+LA
Sbjct: 8 ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKI---ANPVEGSTDRQVTITGSAASISLA 64
Query: 770 QYLINM 775
QYLIN+
Sbjct: 65 QYLINV 70
Score = 34.3 bits (77), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLI 56
+G IIG+ G + ++R+ SG++I I++ + +R VT+ GS S+ A LI
Sbjct: 16 IGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLI 68
Score = 34.3 bits (77), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLI 501
+G IIG+ G + ++R+ SG++I I++ + +R VT+ GS S+ A LI
Sbjct: 16 IGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLI 68
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 31/65 (47%), Positives = 44/65 (67%), Gaps = 3/65 (4%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
E+T+PN LIG +IG+ G I EIR++SGA I+I + R +T+TG+ +I+LA
Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI---ANPVEGSSGRQVTITGSAASISLA 65
Query: 325 QYLIN 329
QYLIN
Sbjct: 66 QYLIN 70
Score = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 31/65 (47%), Positives = 44/65 (67%), Gaps = 3/65 (4%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
E+T+PN LIG +IG+ G I EIR++SGA I+I + R +T+TG+ +I+LA
Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI---ANPVEGSSGRQVTITGSAASISLA 65
Query: 770 QYLIN 774
QYLIN
Sbjct: 66 QYLIN 70
Score = 33.1 bits (74), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLI 56
+G IIG+ G + ++R+ SG++I I++ + R VT+ GS S+ A LI
Sbjct: 17 IGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLI 69
Score = 33.1 bits (74), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLI 501
+G IIG+ G + ++R+ SG++I I++ + R VT+ GS S+ A LI
Sbjct: 17 IGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLI 69
>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|C Chain C, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|D Chain D, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
Length = 76
Score = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 42/68 (61%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
EM VP L+GA++GKGG + E ++++GA I+I +R +T+TG+P A A
Sbjct: 6 EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65
Query: 325 QYLINMSV 332
QYLI+ V
Sbjct: 66 QYLISQRV 73
Score = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 42/68 (61%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
EM VP L+GA++GKGG + E ++++GA I+I +R +T+TG+P A A
Sbjct: 6 EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65
Query: 770 QYLINMSV 777
QYLI+ V
Sbjct: 66 QYLISQRV 73
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDS-----STPERIVTVIGSMDSLFRAFSLITKNI 60
VG+I+GK G+T+ + +E +G++I IS T R VT+ GS + A LI++ +
Sbjct: 14 VGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV 73
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDS-----STPERIVTVIGSMDSLFRAFSLITKNI 505
VG+I+GK G+T+ + +E +G++I IS T R VT+ GS + A LI++ +
Sbjct: 14 VGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV 73
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 57.4 bits (137), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
++T+P +L G++IGKGG +I +IR SGA I+I DR IT+TGT D I A
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 73
Query: 325 QYLINMSVE 333
QYL+ SV+
Sbjct: 74 QYLLQNSVK 82
Score = 57.4 bits (137), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
++T+P +L G++IGKGG +I +IR SGA I+I DR IT+TGT D I A
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 73
Query: 770 QYLINMSVE 778
QYL+ SV+
Sbjct: 74 QYLLQNSVK 82
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 7 GSIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLITKNIEEF 63
GSIIGK G+ +K++R ESG+ I I + + +RI+T+ G+ D + A L+ +++++
Sbjct: 26 GSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 84
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 452 GSIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLITKNIEEF 508
GSIIGK G+ +K++R ESG+ I I + + +RI+T+ G+ D + A L+ +++++
Sbjct: 26 GSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 84
>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
pdb|1EC6|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
Length = 87
Score = 57.0 bits (136), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 42/68 (61%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
E+ VP L+GA++GKGG + E ++++GA I+I +R +T+TG+P A A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65
Query: 325 QYLINMSV 332
QYLI+ V
Sbjct: 66 QYLISQRV 73
Score = 57.0 bits (136), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 42/68 (61%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
E+ VP L+GA++GKGG + E ++++GA I+I +R +T+TG+P A A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65
Query: 770 QYLINMSV 777
QYLI+ V
Sbjct: 66 QYLISQRV 73
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDS-----STPERIVTVIGSMDSLFRAFSLITKNI 60
VG+I+GK G+T+ + +E +G++I IS T R VT+ GS + A LI++ +
Sbjct: 14 VGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV 73
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDS-----STPERIVTVIGSMDSLFRAFSLITKNI 505
VG+I+GK G+T+ + +E +G++I IS T R VT+ GS + A LI++ +
Sbjct: 14 VGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV 73
>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp
K In Complex With Ssdna
pdb|1ZZI|B Chain B, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp
K In Complex With Ssdna
pdb|1ZZJ|A Chain A, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZJ|B Chain B, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZJ|C Chain C, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZK|A Chain A, Crystal Structure Of The Third Kh Domain Of Hnrnp K At
0.95a Resolution
Length = 82
Score = 57.0 bits (136), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
++T+P +L G++IGKGG +I +IR SGA I+I DR IT+TGT D I A
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 66
Query: 325 QYLINMSVE 333
QYL+ SV+
Sbjct: 67 QYLLQNSVK 75
Score = 57.0 bits (136), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
++T+P +L G++IGKGG +I +IR SGA I+I DR IT+TGT D I A
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 66
Query: 770 QYLINMSVE 778
QYL+ SV+
Sbjct: 67 QYLLQNSVK 75
Score = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 7 GSIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLITKNIEEF 63
GSIIGK G+ +K++R ESG+ I I + + +RI+T+ G+ D + A L+ +++++
Sbjct: 19 GSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 77
Score = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 452 GSIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLITKNIEEF 508
GSIIGK G+ +K++R ESG+ I I + + +RI+T+ G+ D + A L+ +++++
Sbjct: 19 GSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 77
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 40/68 (58%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
E+ VP L+GA++GKGG + E ++++G I+I +R +T+TGTP A A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 325 QYLINMSV 332
QYLI +
Sbjct: 66 QYLITQRI 73
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 40/68 (58%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
E+ VP L+GA++GKGG + E ++++G I+I +R +T+TGTP A A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 770 QYLINMSV 777
QYLI +
Sbjct: 66 QYLITQRI 73
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 5/60 (8%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDS-----STPERIVTVIGSMDSLFRAFSLITKNI 60
VG+I+GK G+T+ + +E +G +I IS T R VT+ G+ + A LIT+ I
Sbjct: 14 VGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAAQYLITQRI 73
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 5/60 (8%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDS-----STPERIVTVIGSMDSLFRAFSLITKNI 505
VG+I+GK G+T+ + +E +G +I IS T R VT+ G+ + A LIT+ I
Sbjct: 14 VGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAAQYLITQRI 73
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/69 (44%), Positives = 43/69 (62%), Gaps = 3/69 (4%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
++T+P +L ++IGKGG +I +IR SGA I+I DR IT+TGT D I A
Sbjct: 17 QVTIPKDLARSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 73
Query: 325 QYLINMSVE 333
QYL+ SV+
Sbjct: 74 QYLLQNSVK 82
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/69 (44%), Positives = 43/69 (62%), Gaps = 3/69 (4%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
++T+P +L ++IGKGG +I +IR SGA I+I DR IT+TGT D I A
Sbjct: 17 QVTIPKDLARSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 73
Query: 770 QYLINMSVE 778
QYL+ SV+
Sbjct: 74 QYLLQNSVK 82
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 8 SIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLITKNIEEF 63
SIIGK G+ +K++R ESG+ I I + + +RI+T+ G+ D + A L+ +++++
Sbjct: 27 SIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 84
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 453 SIIGKSGETVKKLREESGSKIYISD--SSTPERIVTVIGSMDSLFRAFSLITKNIEEF 508
SIIGK G+ +K++R ESG+ I I + + +RI+T+ G+ D + A L+ +++++
Sbjct: 27 SIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 84
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 437 GVQRRMRHIMQGKEVGSIIGKSGETVKKLREESGSKIYISDSS-----TPERIVTVIGSM 491
G Q ++ ++ GSIIGK G+T+ +L++E+G+ I +S S T ER+ + G++
Sbjct: 3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62
Query: 492 DSLFRAFSLITKNIEEFHKNQNK 514
++L I + I E +N K
Sbjct: 63 EALNAVHGFIAEKIREMPQNVAK 85
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 5/68 (7%)
Query: 7 GSIIGKSGETVKKLREESGSKIYISDSS-----TPERIVTVIGSMDSLFRAFSLITKNIE 61
GSIIGK G+T+ +L++E+G+ I +S S T ER+ + G++++L I + I
Sbjct: 18 GSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIR 77
Query: 62 EFHKNQNK 69
E +N K
Sbjct: 78 EMPQNVAK 85
Score = 34.3 bits (77), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAI 321
++ +P+ G++IGKGG I +++K +GA I++ +R + GT +A+
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65
Score = 34.3 bits (77), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAI 766
++ +P+ G++IGKGG I +++K +GA I++ +R + GT +A+
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65
Score = 33.5 bits (75), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPD 319
++ VPN G +IGKGG + I + SGA +++ N R +T++G P+
Sbjct: 107 KIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQN-RVVTVSGEPE 160
Score = 33.5 bits (75), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPD 764
++ VPN G +IGKGG + I + SGA +++ N R +T++G P+
Sbjct: 107 KIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQN-RVVTVSGEPE 160
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
E VP+ ++G +IG+GG +I I++ SG I+I +R+ +TGTP+++ A
Sbjct: 18 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPESVQSA 74
Query: 325 QYLINMSVELLRAN 338
+ L++ VE R+
Sbjct: 75 KRLLDQIVEKGRSG 88
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
E VP+ ++G +IG+GG +I I++ SG I+I +R+ +TGTP+++ A
Sbjct: 18 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPESVQSA 74
Query: 770 QYLINMSVELLRAN 783
+ L++ VE R+
Sbjct: 75 KRLLDQIVEKGRSG 88
Score = 38.9 bits (89), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 2/59 (3%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSS--TPERIVTVIGSMDSLFRAFSLITKNIEE 62
VG IIG+ GE + ++++ESG KI I+ S PER + G+ +S+ A L+ + +E+
Sbjct: 26 VGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK 84
Score = 38.9 bits (89), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 2/59 (3%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSS--TPERIVTVIGSMDSLFRAFSLITKNIEE 507
VG IIG+ GE + ++++ESG KI I+ S PER + G+ +S+ A L+ + +E+
Sbjct: 26 VGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK 84
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 437 GVQRRMRHIMQGKEVGSIIGKSGETVKKLREESGSKIYISDSS-----TPERIVTVIGSM 491
G Q ++ ++ GSIIGK G+T+ +L++E+G+ I +S S T ER+ + G++
Sbjct: 3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62
Query: 492 DSLFRAFSLITKNIEEFHKNQNK 514
++L I + I E +N K
Sbjct: 63 EALNAVHGFIAEKIREXPQNVAK 85
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 5/68 (7%)
Query: 7 GSIIGKSGETVKKLREESGSKIYISDSS-----TPERIVTVIGSMDSLFRAFSLITKNIE 61
GSIIGK G+T+ +L++E+G+ I +S S T ER+ + G++++L I + I
Sbjct: 18 GSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIR 77
Query: 62 EFHKNQNK 69
E +N K
Sbjct: 78 EXPQNVAK 85
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAI 321
++ +P+ G++IGKGG I +++K +GA I++ +R + GT +A+
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAI 766
++ +P+ G++IGKGG I +++K +GA I++ +R + GT +A+
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65
Score = 33.9 bits (76), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPD 319
++ VPN G +IGKGG + I + SGA +++ N R +T++G P+
Sbjct: 107 KIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPDGINLQN-RVVTVSGEPE 160
Score = 33.9 bits (76), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPD 764
++ VPN G +IGKGG + I + SGA +++ N R +T++G P+
Sbjct: 107 KIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPDGINLQN-RVVTVSGEPE 160
>pdb|1J4W|A Chain A, Complex Of The Kh3 And Kh4 Domains Of Fbp With A
Single_stranded 29mer Dna Oligonucleotide From The Fuse
Element Of The C-Myc Oncogene
Length = 174
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLIT 57
VG +IG++GE +KK++ ++G +I D +TPERI + G D A +IT
Sbjct: 14 VGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIIT 67
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLIT 502
VG +IG++GE +KK++ ++G +I D +TPERI + G D A +IT
Sbjct: 14 VGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIIT 67
Score = 35.8 bits (81), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 30/67 (44%)
Query: 266 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALAQ 325
VP G +IGKGG I I + SGA I + N + T+ GTP I A+
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYAR 167
Query: 326 YLINMSV 332
LI +
Sbjct: 168 QLIEEKI 174
Score = 35.8 bits (81), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 30/67 (44%)
Query: 711 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALAQ 770
VP G +IGKGG I I + SGA I + N + T+ GTP I A+
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYAR 167
Query: 771 YLINMSV 777
LI +
Sbjct: 168 QLIEEKI 174
Score = 33.5 bits (75), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 5 EVGSIIGKSGETVKKLREESGSKIYISDSSTPE-----RIVTVIGSMDSLFRAFSLITKN 59
+ G IIGK GET+K + ++SG++I + + P ++ T+ G+ + A LI +
Sbjct: 114 KTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK 173
Query: 60 I 60
I
Sbjct: 174 I 174
Score = 33.5 bits (75), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 450 EVGSIIGKSGETVKKLREESGSKIYISDSSTPE-----RIVTVIGSMDSLFRAFSLITKN 504
+ G IIGK GET+K + ++SG++I + + P ++ T+ G+ + A LI +
Sbjct: 114 KTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK 173
Query: 505 I 505
I
Sbjct: 174 I 174
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 41/65 (63%), Gaps = 3/65 (4%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
E VP+ ++G +IG+GG +I +I++ SG ++I +R++++TG P+++ A
Sbjct: 19 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGAPESVQKA 75
Query: 325 QYLIN 329
+ +++
Sbjct: 76 KMMLD 80
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 41/65 (63%), Gaps = 3/65 (4%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
E VP+ ++G +IG+GG +I +I++ SG ++I +R++++TG P+++ A
Sbjct: 19 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGAPESVQKA 75
Query: 770 QYLIN 774
+ +++
Sbjct: 76 KMMLD 80
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 36/53 (67%), Gaps = 2/53 (3%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSS--TPERIVTVIGSMDSLFRAFSLI 56
VG IIG+ GE + K++++SG K+ IS S PER V++ G+ +S+ +A ++
Sbjct: 27 VGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMML 79
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 36/53 (67%), Gaps = 2/53 (3%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSS--TPERIVTVIGSMDSLFRAFSLI 501
VG IIG+ GE + K++++SG K+ IS S PER V++ G+ +S+ +A ++
Sbjct: 27 VGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMML 79
>pdb|2HH3|A Chain A, Solution Structure Of The Third Kh Domain Of Ksrp
Length = 106
Score = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 63
VG +IG+SGE +KK++ ++G +I D + PE+I ++G D A +I ++
Sbjct: 22 VGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL 81
Score = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 508
VG +IG+SGE +KK++ ++G +I D + PE+I ++G D A +I ++
Sbjct: 22 VGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL 81
>pdb|4B8T|A Chain A, Rna Binding Protein Solution Structure Of The Third Kh
Domain Of Ksrp In Complex With The G-rich Target
Sequence
Length = 106
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 63
VG +IG+SGE +KK++ ++G +I D + PE+I ++G D A +I ++
Sbjct: 22 VGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL 81
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 508
VG +IG+SGE +KK++ ++G +I D + PE+I ++G D A +I ++
Sbjct: 22 VGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL 81
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 56/124 (45%), Gaps = 9/124 (7%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSSTPE---RIVTVIGSMDSLFRAFSLITKNIEE 62
VG+IIGK G+ +K+L + + I I+ TP+ R+V + G ++ F+A I ++E
Sbjct: 14 VGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKE 73
Query: 63 FHKNQNKHLGGNGESQLIQLRLIVPASQCXXXXXXXXXXXXXXRETSGASVYVASDMLPN 122
++ G E ++ + VPAS + + A V V D P+
Sbjct: 74 ------ENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPD 127
Query: 123 STER 126
++
Sbjct: 128 ENDQ 131
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 56/124 (45%), Gaps = 9/124 (7%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSSTPE---RIVTVIGSMDSLFRAFSLITKNIEE 507
VG+IIGK G+ +K+L + + I I+ TP+ R+V + G ++ F+A I ++E
Sbjct: 14 VGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKE 73
Query: 508 FHKNQNKHLGGNGESQLIQLRLIVPASQCXXXXXXXXXXXXXXRETSGASVYVASDMLPN 567
++ G E ++ + VPAS + + A V V D P+
Sbjct: 74 ------ENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPD 127
Query: 568 STER 571
++
Sbjct: 128 ENDQ 131
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
++ +P + +GA+IGK G I ++ + + A I+I R + +TG P+A A
Sbjct: 6 QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKV--RMVIITGPPEAQFKA 63
Query: 325 Q 325
Q
Sbjct: 64 Q 64
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
++ +P + +GA+IGK G I ++ + + A I+I R + +TG P+A A
Sbjct: 6 QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKV--RMVIITGPPEAQFKA 63
Query: 770 Q 770
Q
Sbjct: 64 Q 64
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 63
VG +IG+SGE +KK++ ++G +I D + PE+I ++G D A +I ++
Sbjct: 102 VGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL 161
Query: 64 H 64
Sbjct: 162 R 162
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 508
VG +IG+SGE +KK++ ++G +I D + PE+I ++G D A +I ++
Sbjct: 102 VGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL 161
Query: 509 H 509
Sbjct: 162 R 162
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 5 EVGSIIGKSGETVKKLREESGSK-IYISDSS 34
+ G +IGK GET+K+L+E +G K I I D S
Sbjct: 12 KAGLVIGKGGETIKQLQERAGVKMILIQDGS 42
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 450 EVGSIIGKSGETVKKLREESGSK-IYISDSS 479
+ G +IGK GET+K+L+E +G K I I D S
Sbjct: 12 KAGLVIGKGGETIKQLQERAGVKMILIQDGS 42
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 37.7 bits (86), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 324
+++VP +G +IG+GG I I K SGA I + R I ++GT +A A
Sbjct: 18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS-RLIKISGTQKEVAAA 76
Query: 325 QYLI 328
++LI
Sbjct: 77 KHLI 80
Score = 37.7 bits (86), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIALA 769
+++VP +G +IG+GG I I K SGA I + R I ++GT +A A
Sbjct: 18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS-RLIKISGTQKEVAAA 76
Query: 770 QYLI 773
++LI
Sbjct: 77 KHLI 80
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 4 KEVGSIIGKSGETVKKLREESGSKIYISDSSTP----ERIVTVIGSMDSLFRAFSLITKN 59
+ VG IIG+ GET++ + + SG+KI S R++ + G+ + A LI +
Sbjct: 24 RSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEK 83
Query: 60 IEE 62
+ E
Sbjct: 84 VSE 86
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 449 KEVGSIIGKSGETVKKLREESGSKIYISDSSTP----ERIVTVIGSMDSLFRAFSLITKN 504
+ VG IIG+ GET++ + + SG+KI S R++ + G+ + A LI +
Sbjct: 24 RSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEK 83
Query: 505 IEE 507
+ E
Sbjct: 84 VSE 86
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 36.2 bits (82), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 265 EMT--VPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIA 322
EMT +P G VIG+GG + I + +GA + I N + + G+P I
Sbjct: 8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQID 67
Query: 323 LAQYLINMSVE 333
A+ LI +E
Sbjct: 68 HAKQLIEEKIE 78
Score = 36.2 bits (82), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 710 EMT--VPNELIGAVIGKGGTKIFEIRKISGAMIRIXXXXXXXXXXNDRTITMTGTPDAIA 767
EMT +P G VIG+GG + I + +GA + I N + + G+P I
Sbjct: 8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQID 67
Query: 768 LAQYLINMSVE 778
A+ LI +E
Sbjct: 68 HAKQLIEEKIE 78
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 5 EVGSIIGKSGETVKKLREESGSKIYISDSSTPE-----RIVTVIGSMDSLFRAFSLITKN 59
+ G +IG+ GE VK + +++G+ + IS P ++ + GS + A LI +
Sbjct: 17 KCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEK 76
Query: 60 IE 61
IE
Sbjct: 77 IE 78
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 450 EVGSIIGKSGETVKKLREESGSKIYISDSSTPE-----RIVTVIGSMDSLFRAFSLITKN 504
+ G +IG+ GE VK + +++G+ + IS P ++ + GS + A LI +
Sbjct: 17 KCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEK 76
Query: 505 IE 506
IE
Sbjct: 77 IE 78
>pdb|2QND|A Chain A, Crystal Structure Of The Kh1-Kh2 Domains From Human
Fragile X Mental Retardation Protein
pdb|2QND|B Chain B, Crystal Structure Of The Kh1-Kh2 Domains From Human
Fragile X Mental Retardation Protein
Length = 144
Score = 33.5 bits (75), Expect = 0.52, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 266 MTVPNELIGAVIGKGGTKIFEIRKISGAM-IRIXXXXXXXXXXNDRTI--TMTGTPDAIA 322
+ VP L+G VIGK G I EI SG + +RI + + GT D+IA
Sbjct: 71 IQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGXVPFVFVGTKDSIA 130
Query: 323 LAQYLINMSVELLR 336
A L++ + L+
Sbjct: 131 NATVLLDYHLNYLK 144
Score = 33.5 bits (75), Expect = 0.52, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 711 MTVPNELIGAVIGKGGTKIFEIRKISGAM-IRIXXXXXXXXXXNDRTI--TMTGTPDAIA 767
+ VP L+G VIGK G I EI SG + +RI + + GT D+IA
Sbjct: 71 IQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGXVPFVFVGTKDSIA 130
Query: 768 LAQYLINMSVELLR 781
A L++ + L+
Sbjct: 131 NATVLLDYHLNYLK 144
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 32.3 bits (72), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 7/43 (16%)
Query: 5 EVGSIIGKSGETVKKLREESGSK-IYISDSS------TPERIV 40
+ G +IGK GET+K+L+E +G K I I D S P RI+
Sbjct: 24 KAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII 66
Score = 32.3 bits (72), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 7/43 (16%)
Query: 450 EVGSIIGKSGETVKKLREESGSK-IYISDSS------TPERIV 485
+ G +IGK GET+K+L+E +G K I I D S P RI+
Sbjct: 24 KAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII 66
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%)
Query: 5 EVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLITKNIE 61
++ +IGK G ++ L EE+G+ I I D T + T R IT IE
Sbjct: 570 KIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKIAATDGEKAKHAIRRIEEITAEIE 626
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%)
Query: 450 EVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLITKNIE 506
++ +IGK G ++ L EE+G+ I I D T + T R IT IE
Sbjct: 570 KIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKIAATDGEKAKHAIRRIEEITAEIE 626
>pdb|2CXC|A Chain A, Crystal Structure Of Archaeal Transcription Termination
Factor Nusa
pdb|2CY1|A Chain A, Crystal Structure Of Ape1850
Length = 144
Score = 29.6 bits (65), Expect = 7.2, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 441 RMRHIMQGKEVGSIIGKSGETVKKLREESGSKIYISD-SSTPERIVTVIGSMDSLFRAFS 499
R+ ++ E G IG+ G +K LRE G I + + SS ERIV +LF
Sbjct: 37 RLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSDLERIVK------NLFPGVK 90
Query: 500 LITKNIEE 507
+ + N+ E
Sbjct: 91 IESINVRE 98
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 29.6 bits (65), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 20/26 (76%)
Query: 5 EVGSIIGKSGETVKKLREESGSKIYI 30
+ G +IGK GET+K+L+E +G K+ +
Sbjct: 25 KAGLVIGKGGETIKQLQERAGVKMVM 50
Score = 29.6 bits (65), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 20/26 (76%)
Query: 450 EVGSIIGKSGETVKKLREESGSKIYI 475
+ G +IGK GET+K+L+E +G K+ +
Sbjct: 25 KAGLVIGKGGETIKQLQERAGVKMVM 50
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
0.312 0.132 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,110,022
Number of Sequences: 62578
Number of extensions: 583423
Number of successful extensions: 1222
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1056
Number of HSP's gapped (non-prelim): 136
length of query: 914
length of database: 14,973,337
effective HSP length: 108
effective length of query: 806
effective length of database: 8,214,913
effective search space: 6621219878
effective search space used: 6621219878
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: 56 (26.2 bits)