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= 012307
(466 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 = 66.2 bits (160), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 46/137 (33%), Positives = 78/137 (56%), Gaps = 18/137 (13%)
Query: 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSP 139
R+++ +VGSIIG+KGE +KK E++ ARI + +G + P+RI+ ++G
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAG---------- 54
Query: 140 AMDAAVRVFKRVSGLPENDVDAKASGAAFCS-----VRLLVPSTQAINLIGKQGSLIKSI 194
+A + F + E D+ + + + S +RL+VP++Q +LIGK G IK I
Sbjct: 55 PTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEI 114
Query: 195 QENSGASVRVLSADEAP 211
+E++GA V+V + D P
Sbjct: 115 RESTGAQVQV-AGDMLP 130
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 24/35 (68%)
Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRV 204
++RLL+ + ++IGK+G +K ++E SGA + +
Sbjct: 6 TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI 40
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 45/85 (52%), Gaps = 5/85 (5%)
Query: 330 SALGRASGPIVT-QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEI 388
++ G GPI+T Q+T IP A IIG GG I+ IR SGA I + E ++
Sbjct: 4 NSYGDLGGPIITTQVT----IPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDR 59
Query: 389 TVEIKGTSSQVQLAQQLIQEYMNNH 413
+ I GT Q+Q AQ L+Q + +
Sbjct: 60 IITITGTQDQIQNAQYLLQNSVKQY 84
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM 223
G + ++ +P A ++IGK G IK I+ SGAS+++ + P +ED RI+ +
Sbjct: 10 GGPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI----DEPLEGSED-RIITI 63
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 27/42 (64%)
Query: 91 SIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
SIIG+ G+ IK+ ++ A IK+ + S DRI+ I+G ++
Sbjct: 27 SIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 68
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 42/136 (30%), Positives = 68/136 (50%), Gaps = 16/136 (11%)
Query: 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPD---RIVLISGKEEPEA 135
+ ++ +P VG+IIG+KG+ IK+ A IK+ P +PD R+V+I+G PEA
Sbjct: 4 MVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKI--APPETPDSKVRMVIITG--PPEA 59
Query: 136 PVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQ 195
A R++ ++ EN K +R VP++ A +IGK G + +Q
Sbjct: 60 ----QFKAQGRIYGKLK--EENFFGPKEEVKLETHIR--VPASAAGRVIGKGGKTVNELQ 111
Query: 196 ENSGASVRVLSADEAP 211
+ A V V+ D+ P
Sbjct: 112 NLTAAEV-VVPRDQTP 126
Score = 28.9 bits (63), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 347 MQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDE---ITVEIKGTSSQVQLAQ 403
+++P S A +IG GG ++ ++ + A + V + PDE + V+I G Q+AQ
Sbjct: 89 IRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQ-TPDENDQVIVKIIGHFYASQMAQ 147
Query: 404 QLIQEYMNNHKE 415
+ I++ + K+
Sbjct: 148 RKIRDILAQVKQ 159
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 32/84 (38%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 331 ALGRASGPIVT-QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEIT 389
+ G GPI+T Q+T IP A IIG GG I+ IR SGA I + E ++
Sbjct: 5 SYGDLGGPIITTQVT----IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRI 60
Query: 390 VEIKGTSSQVQLAQQLIQEYMNNH 413
+ I GT Q+Q AQ L+Q + +
Sbjct: 61 ITITGTQDQIQNAQYLLQNSVKQY 84
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 32/52 (61%)
Query: 81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
++ +P GSIIG+ G+ IK+ ++ A IK+ + S DRI+ I+G ++
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 68
Score = 32.0 bits (71), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM 223
G + ++ +P A ++IGK G IK I+ SGAS+++ + P +ED RI+ +
Sbjct: 10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSED-RIITI 63
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/80 (40%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 335 ASGPIVT-QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIK 393
A GPI+T Q+T IP A IIG GG I+ IR SGA I + E ++ + I
Sbjct: 2 AMGPIITTQVT----IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT 57
Query: 394 GTSSQVQLAQQLIQEYMNNH 413
GT Q+Q AQ L+Q + +
Sbjct: 58 GTQDQIQNAQYLLQNSVKQY 77
Score = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 32/52 (61%)
Query: 81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
++ +P GSIIG+ G+ IK+ ++ A IK+ + S DRI+ I+G ++
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 61
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 5/56 (8%)
Query: 168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM 223
+ ++ +P A ++IGK G IK I+ SGAS+++ + P +ED RI+ +
Sbjct: 6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSED-RIITI 56
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 43/153 (28%), Positives = 75/153 (49%), Gaps = 18/153 (11%)
Query: 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSP---DRIVLISGKEEPEAP 136
++++P GSIIG+ G+ I + ++T A IK+ P +R+ LI G E
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67
Query: 137 VSPAMDAAVRVFKR-------VSGL-PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQG 188
V + +R + VS L P+ V+ + V+++VP++ A +IGK G
Sbjct: 68 VHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRAN----QVKIIVPNSTAGLIIGKGG 123
Query: 189 SLIKSIQENSGASVRVLSADEAPFYVTEDERIV 221
+ +K+I E SGA V++ + P + R+V
Sbjct: 124 ATVKAIMEQSGAWVQL---SQKPDGINLQNRVV 153
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQ 224
+++L+PS A ++IGK G I +Q+ +GA++++ + + FY ER+ +Q
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD--FYPGTTERVCLIQ 59
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGP--VSSPDRIVLISGKEEPE 134
++IVP G IIG+ G +K E + A +++ P ++ +R+V +SG EPE
Sbjct: 107 KIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSG--EPE 160
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/158 (26%), Positives = 74/158 (46%), Gaps = 28/158 (17%)
Query: 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSP---DRIVLISGKEEP--- 133
++++P GSIIG+ G+ I + ++T A IK+ P +R+ LI G E
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67
Query: 134 ----------EAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINL 183
E P + A V + + P+ V+ + V+++VP++ A +
Sbjct: 68 VHGFIAEKIREXPQNVAKTEPVSILQ-----PQTTVNPDRAN----QVKIIVPNSTAGLI 118
Query: 184 IGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIV 221
IGK G+ +K+I E SGA V++ + P + R+V
Sbjct: 119 IGKGGATVKAIXEQSGAWVQL---SQKPDGINLQNRVV 153
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQ 224
+++L+PS A ++IGK G I +Q+ +GA++++ + + FY ER+ +Q
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD--FYPGTTERVCLIQ 59
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGP--VSSPDRIVLISGKEEPE 134
++IVP G IIG+ G +K E + A +++ P ++ +R+V +SG EPE
Sbjct: 107 KIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSG--EPE 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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 37/142 (26%), Positives = 57/142 (40%), Gaps = 16/142 (11%)
Query: 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEA 135
G + + +P VG +IGR GE+IKK D RI+ ++P+RI I+G P
Sbjct: 1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITG---PPD 57
Query: 136 PVSPAMDAAVRVFKRVSGLPENDVDAKASG-------------AAFCSVRLLVPSTQAIN 182
A + + + V G +VP+ +
Sbjct: 58 RAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGL 117
Query: 183 LIGKQGSLIKSIQENSGASVRV 204
+IGK G IKSI + SGA + +
Sbjct: 118 IIGKGGETIKSISQQSGARIEL 139
Score = 35.8 bits (81), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 349 IPISYAEDIIGVGGTSIENIRRTSGAIITVQES---RGLPDEITVEIKGTSSQVQLAQQL 405
+P IIG GG +I++I + SGA I +Q + P+ I+GT Q+ A+QL
Sbjct: 110 VPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQL 169
Query: 406 IQEYM 410
I+E +
Sbjct: 170 IEEKI 174
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 24/43 (55%)
Query: 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPD 122
F IVP K G IIG+ GE IK + + ARI++ P + D
Sbjct: 106 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNAD 148
>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 = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 37/49 (75%), Gaps = 2/49 (4%)
Query: 81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
R+++ +VGSIIG+KGE +K+ E++ ARI + +G +SP+RI+ ++G
Sbjct: 6 RLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NSPERIITLTG 52
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRV 204
++RLL+ + ++IGK+G +K I+E SGA + +
Sbjct: 4 TIRLLMHGKEVGSIIGKKGESVKRIREESGARINI 38
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 37/54 (68%), Gaps = 2/54 (3%)
Query: 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
G R+++ +VGSIIG+KGE +K+ E++ ARI + +G + P+RI+ ++G
Sbjct: 1 GILTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG--NCPERIITLTG 52
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRV 204
++RLL+ + ++IGK+G +K I+E SGA + +
Sbjct: 4 TIRLLMHGKEVGSIIGKKGESVKRIREESGARINI 38
>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 = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 35/49 (71%), Gaps = 2/49 (4%)
Query: 81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
R++ +VGSIIG+KGE +KK E++ ARI + +G + P+RI+ ++G
Sbjct: 8 RLLXHGKEVGSIIGKKGESVKKXREESGARINISEG--NCPERIITLAG 54
Score = 28.1 bits (61), Expect = 9.7, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRV 204
++RLL + ++IGK+G +K +E SGA + +
Sbjct: 6 TIRLLXHGKEVGSIIGKKGESVKKXREESGARINI 40
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 329 SSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQ-ESRGLPDE 387
SS LG P T +T+ ++P IIG GG I I++ SG + + +S GLP E
Sbjct: 2 SSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP-E 60
Query: 388 ITVEIKGTSSQVQLAQQLIQEYMNNHK 414
+V + G VQ A+ ++ + ++ +
Sbjct: 61 RSVSLTGAPESVQKAKMMLDDIVSRGR 87
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 84 VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
VP VG IIGR GE I K +D+ ++++ P+R V ++G E
Sbjct: 22 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPE 70
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 36.2 bits (82), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 341 TQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV-QESRG-LPDEITVEIKGTSSQ 398
T + + + +P IIG GG +I +I + SGA IT +ES G L ++I GT +
Sbjct: 13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72
Query: 399 VQLAQQLIQEYMNNHKE 415
V A+ LI E ++ +E
Sbjct: 73 VAAAKHLILEKVSEDEE 89
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 35.8 bits (81), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%)
Query: 338 PIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSS 397
P+ +Q T + IP + IIG G +I IR+ SGA I + V I G+++
Sbjct: 1 PLGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA 60
Query: 398 QVQLAQQLIQEYMNNHK 414
+ LAQ LI +++ K
Sbjct: 61 SISLAQYLINARLSSEK 77
>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 = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 25/46 (54%)
Query: 84 VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
VP VG +IGR GE+IKK D RI+ + P++I I G
Sbjct: 17 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG 62
>pdb|2HH3|A Chain A, Solution Structure Of The Third Kh Domain Of Ksrp
Length = 106
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 25/46 (54%)
Query: 84 VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
VP VG +IGR GE+IKK D RI+ + P++I I G
Sbjct: 17 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG 62
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 25/46 (54%)
Query: 84 VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
VP VG +IGR GE+IKK D RI+ + P++I I G
Sbjct: 97 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG 142
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 37/140 (26%), Positives = 65/140 (46%), Gaps = 22/140 (15%)
Query: 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL---DGP----VSSPDRIVLISGKE 131
V +++P K G +IG+ GE IK+ E RA +K++ DG V P RI+
Sbjct: 3 VQEIMIPAGKAGLVIGKGGETIKQLQE--RAGVKMILIQDGSQNTNVDKPLRII-----G 55
Query: 132 EPEAPVSPAMDAAVRVFKR--VSGLPE-NDVDAKASGAAFCSVRLLVPSTQAINLIGKQG 188
+P V A + + + + G + N+ ++ G + + VP +IG+ G
Sbjct: 56 DP-YKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGG----IDVPVPRHSVGVVIGRSG 110
Query: 189 SLIKSIQENSGASVRVLSAD 208
+IK IQ ++G ++ D
Sbjct: 111 EMIKKIQNDAGVRIQFKQDD 130
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 346 TMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQES---RGLPDEITVEIKGTSSQVQLA 402
T IP +IG GG +++ I + +GA + + G P+ I+G+ Q+ A
Sbjct: 10 TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHA 69
Query: 403 QQLIQE 408
+QLI+E
Sbjct: 70 KQLIEE 75
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQ-ESRGLPDEITVEIKGTSSQVQL 401
+T+ ++P IIG GG I I++ SG I + +S GLP E + + GT VQ
Sbjct: 15 MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP-ERSCMLTGTPESVQS 73
Query: 402 AQQLIQEYMNNHKESITS 419
A++L+ + + + +S
Sbjct: 74 AKRLLDQIVEKGRSGPSS 91
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 84 VPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132
VP VG IIGR GE I + +++ +I++ P+R +++G E
Sbjct: 21 VPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPE 69
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 84 VPVLKVGSIIGRKGELIKKTCEDTRARIKVLD 115
+PV K+G +IG K ++I + EDT A I + D
Sbjct: 604 IPVDKIGEVIGPKRQMINQIQEDTGAEITIED 635
>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 = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 82 MIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISG 129
+ +P +G IIGR+G I + + + A+IK+ + S DR V I+G
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITG 56
Score = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%)
Query: 347 MQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLI 406
+ IP IIG G I IR+ SGA I + + V I G+++ + LAQ LI
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLI 68
>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 = 3.9, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 6/57 (10%)
Query: 77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL---DGPVSS-PDRIVLISG 129
+ V +++P K G +IG+ GE IK+ E RA +K++ DGP ++ D+ + I+G
Sbjct: 14 NAVQEIMIPASKAGLVIGKGGETIKQLQE--RAGVKMVMIQDGPQNTGADKPLRITG 68
Score = 28.9 bits (63), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 29/51 (56%), Gaps = 6/51 (11%)
Query: 173 LLVPSTQAINLIGKQGSLIKSIQENSGASVRVL------SADEAPFYVTED 217
+++P+++A +IGK G IK +QE +G + ++ + + P +T D
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD 69
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 55/116 (47%), Gaps = 25/116 (21%)
Query: 92 IIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRV 151
II G LI+ +D R RI + DR VL+ +PE A+R +
Sbjct: 42 IITENGNLIRDIAKDIRKRI------IIRSDRSVLM----DPEK--------AIRKIHEI 83
Query: 152 SGLPENDVDAKASGAAFCSV--RLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL 205
+PE +AK + +F V +++ + + +IGK GS + I +N+G + ++L
Sbjct: 84 --VPE---EAKITNISFDDVTCEVIIEARKPGLVIGKYGSTSREIVKNTGWAPKIL 134
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 84 VPVLKVGSIIGRKGELIKKTCEDTRARIKVLD 115
+PV K+G +IG K + I + EDT A I + D
Sbjct: 604 IPVDKIGEVIGPKRQXINQIQEDTGAEITIED 635
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 0.129 0.360
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,574,350
Number of Sequences: 62578
Number of extensions: 428686
Number of successful extensions: 987
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 905
Number of HSP's gapped (non-prelim): 77
length of query: 466
length of database: 14,973,337
effective HSP length: 102
effective length of query: 364
effective length of database: 8,590,381
effective search space: 3126898684
effective search space used: 3126898684
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)