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= 019747
(336 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 115 bits (287), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 66/178 (37%), Positives = 107/178 (60%), Gaps = 26/178 (14%)
Query: 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
+++ L+ + AG++IGKGG TI Q ++GA I+LS+S +F+PGTT+R+ +I GTI E L
Sbjct: 7 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI-EAL 65
Query: 96 RAVDLVIDKLLTELHAE------------------DQADDVGTKTKLRLIVPNSSCGSII 137
AV I + + E+ D+A+ V ++IVPNS+ G II
Sbjct: 66 NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQV------KIIVPNSTAGLII 119
Query: 138 GKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195
GK GAT+K+ M+ S A +++S+ L +R+VT++G ++ +A+ELI+ K+ ED
Sbjct: 120 GKGGATVKAIMEQSGAWVQLSQKPDG-INLQNRVVTVSGEPEQNRKAVELIIQKIQED 176
Score = 65.5 bits (158), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 53/210 (25%), Positives = 89/210 (42%), Gaps = 38/210 (18%)
Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
+G++ L++++P+ + GSIIGK G TI ++ A IK+S+ Y G +R+ + GT
Sbjct: 2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61
Query: 178 LDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGXXXXXXXXXXHNTAA 237
+ E + A+ G MP A
Sbjct: 62 I-EALNAVH-----------------------GFIAEKIREMP-------------QNVA 84
Query: 238 HYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGD 297
P + DR N + I V + G ++G+GG + I + SGA +++S + D
Sbjct: 85 KTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD 144
Query: 298 FFSGTSERKVTISGPQRSIRTAESMIMQKV 327
+ R VT+SG R A +I+QK+
Sbjct: 145 GIN-LQNRVVTVSGEPEQNRKAVELIIQKI 173
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 112 bits (279), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 58/171 (33%), Positives = 103/171 (60%), Gaps = 12/171 (7%)
Query: 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL 95
+++ L+ + AG++IGKGG TI Q ++GA I+LS+S +F+PGTT+R+ +I GTI+ +
Sbjct: 7 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALN 66
Query: 96 RAVDLVIDKLLTELHAEDQADDVGT-----------KTKLRLIVPNSSCGSIIGKAGATI 144
+ +K+ + + V ++++IVPNS+ G IIGK GAT+
Sbjct: 67 AVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATV 126
Query: 145 KSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195
K+ + S A +++S+ L +R+VT++G ++ +A+ELI+ K+ ED
Sbjct: 127 KAIXEQSGAWVQLSQKPDG-INLQNRVVTVSGEPEQNRKAVELIIQKIQED 176
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 51/210 (24%), Positives = 92/210 (43%), Gaps = 38/210 (18%)
Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
+G++ L++++P+ + GSIIGK G TI ++ A IK+S+ Y G +R+ + GT
Sbjct: 2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61
Query: 178 LDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGXXXXXXXXXXHNTAA 237
+ E + A+ + + + + T P + T
Sbjct: 62 I-EALNAVHGFIAEKIREXPQNVAKTEPVSI----------------------LQPQTTV 98
Query: 238 HYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGD 297
+ DR N + I V + G ++G+GG + I + SGA +++S + D
Sbjct: 99 N--------------PDRANQVKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPD 144
Query: 298 FFSGTSERKVTISGPQRSIRTAESMIMQKV 327
+ R VT+SG R A +I+QK+
Sbjct: 145 GIN-LQNRVVTVSGEPEQNRKAVELIIQKI 173
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 75.1 bits (183), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 47/162 (29%), Positives = 89/162 (54%), Gaps = 16/162 (9%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
IR L+ G++IGK G ++ + +SGARI +S + +RII ++G + I +
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-----CPERIITLAGPTNAIFK 61
Query: 97 AVDLVIDKLLTELHAEDQADDVGTK--TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154
A ++IDKL ++ + ++ LRL+VP S CGS+IGK G IK + + A
Sbjct: 62 AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQ 121
Query: 155 IKIS--RLDHSYYGLNDRLVTLTG---TLDEQMRALELILLK 191
++++ L +S +R +T+ G ++ E ++ + +++L+
Sbjct: 122 VQVAGDMLPNS----TERAITIAGIPQSIIECVKQICVVMLE 159
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/193 (26%), Positives = 87/193 (45%), Gaps = 53/193 (27%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
+RL++ GSIIGK G ++K ++S A R++ S +R++TL G + +
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGA-----RINISEGNCPERIITLAGPTNAIFK 61
Query: 184 ALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGXXXXXXXXXXHNTAAHYGPNM 243
A +I+ KL ED S +MT ++TAA P
Sbjct: 62 AFAMIIDKLEED--ISSSMT-----------------------------NSTAASRPP-- 88
Query: 244 GGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTS 303
+L + V G ++G+GG I EI + +GA+++V+ GD ++
Sbjct: 89 -------------VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVA--GDMLPNST 133
Query: 304 ERKVTISGPQRSI 316
ER +TI+G +SI
Sbjct: 134 ERAITIAGIPQSI 146
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 27 SSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
S+ + P +R +V G++IGKGG I + + +GA++Q+ + + P +T+R I
Sbjct: 81 STAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQV--AGDMLPNSTERAIT 138
Query: 87 ISGTIDEILRAVDLVIDKLL 106
I+G I+ V + +L
Sbjct: 139 IAGIPQSIIECVKQICVVML 158
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 266 EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQ 325
+ +G ++G+ G ++ ++ + SGARI +S+ ER +T++GP +I A +MI+
Sbjct: 14 KEVGSIIGKKGESVKKMREESGARINISE-----GNCPERIITLAGPTNAIFKAFAMIID 68
Query: 326 KV 327
K+
Sbjct: 69 KL 70
>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 = 63.2 bits (152), Expect = 2e-10, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 48/69 (69%)
Query: 261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAE 320
I V + +G ++G+GG+ ++E +++GARI++S +G+F GT R+VTI+G + + A+
Sbjct: 7 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQ 66
Query: 321 SMIMQKVAY 329
+I Q+V Y
Sbjct: 67 YLISQRVTY 75
Score = 55.1 bits (131), Expect = 5e-08, Method: Composition-based stats.
Identities = 24/54 (44%), Positives = 37/54 (68%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT 90
+ V L GA++GKGG T+ ++Q +GARIQ+S+ EF PGT +R + I+G+
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58
Score = 35.4 bits (80), Expect = 0.045, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
K + + VP + G+I+GK G T+ + + + A I+IS+ G +R VT+TG+
Sbjct: 2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58
>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 = 62.0 bits (149), Expect = 4e-10, Method: Composition-based stats.
Identities = 25/69 (36%), Positives = 48/69 (69%)
Query: 261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAE 320
+ V + +G ++G+GG+ ++E +++GARI++S +G+F GT R+VTI+G + + A+
Sbjct: 7 MAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQ 66
Query: 321 SMIMQKVAY 329
+I Q+V Y
Sbjct: 67 YLISQRVTY 75
Score = 55.1 bits (131), Expect = 5e-08, Method: Composition-based stats.
Identities = 24/54 (44%), Positives = 37/54 (68%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT 90
+ V L GA++GKGG T+ ++Q +GARIQ+S+ EF PGT +R + I+G+
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
K + + VP + G+I+GK G T+ + + + A I+IS+ G +R VT+TG+
Sbjct: 2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 60.1 bits (144), Expect = 2e-09, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 46/67 (68%)
Query: 261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAE 320
I V + +G ++G+GG+ ++E +++G RI++S +G+F GT RKVTI+G + + A+
Sbjct: 7 IAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAAQ 66
Query: 321 SMIMQKV 327
+I Q++
Sbjct: 67 YLITQRI 73
Score = 55.5 bits (132), Expect = 4e-08, Method: Composition-based stats.
Identities = 24/54 (44%), Positives = 36/54 (66%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT 90
+ V L GA++GKGG T+ ++Q +G RIQ+S+ EF PGT +R + I+GT
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGT 58
Score = 35.4 bits (80), Expect = 0.049, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 32/57 (56%)
Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
K + + VP + G+I+GK G T+ + + + I+IS+ G +R VT+TGT
Sbjct: 2 KDVVEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGT 58
>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 = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 54/174 (31%), Positives = 72/174 (41%), Gaps = 29/174 (16%)
Query: 38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTT-DRIIMISGTIDEILR 96
RF V G VIG+ G I Q+ +G RIQ GTT +RI I+G D
Sbjct: 11 RFAV-----GIVIGRNGEMIKKIQNDAGVRIQFKPDD----GTTPERIAQITGPPDRAQH 61
Query: 97 AVDLVIDKLLTELHAEDQADDV------------------GTKTKLRLIVPNSSCGSIIG 138
A +++ D LL + A + G + IVP G IIG
Sbjct: 62 AAEIITD-LLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIG 120
Query: 139 KAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL 192
K G TIKS S A I++ R N +L T+ GT + A +LI K+
Sbjct: 121 KGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 46/200 (23%), Positives = 73/200 (36%), Gaps = 34/200 (17%)
Query: 128 VPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL 187
+P + G +IG+ G IK +D+ I+ D + +R+ +TG D A E+
Sbjct: 9 IPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP---ERIAQITGPPDRAQHAAEI 65
Query: 188 ILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGXXXXXXXXXXHNTAAHYGPNMGGRK 247
I D L S P + GP G ++
Sbjct: 66 IT-----DLLRSVQAGNPGGPG---------------PGGRGRGRGQGNWNMGPPGGLQE 105
Query: 248 FQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKV 307
F V G ++G+GG I ISQ SGARI++ + + +
Sbjct: 106 F-----------NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLF 154
Query: 308 TISGPQRSIRTAESMIMQKV 327
TI G + I A +I +K+
Sbjct: 155 TIRGTPQQIDYARQLIEEKI 174
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 47/73 (64%), Gaps = 5/73 (6%)
Query: 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS 315
T+ LTI + IG ++GR G NI EI Q+SGA+IK+++ G+S R+VTI+G S
Sbjct: 7 THELTI--PNNLIGCIIGRQGANINEIRQMSGAQIKIANP---VEGSSGRQVTITGSAAS 61
Query: 316 IRTAESMIMQKVA 328
I A+ +I +++
Sbjct: 62 ISLAQYLINARLS 74
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 118 VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177
+G++T L +PN+ G IIG+ GA I S A IKI+ + G + R VT+TG+
Sbjct: 2 LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIA---NPVEGSSGRQVTITGS 58
Query: 178 LDEQMRALELILLKLSED 195
A LI +LS +
Sbjct: 59 AASISLAQYLINARLSSE 76
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89
P T + N L G +IG+ G+ IN+ + SGA+I+++ E G++ R + I+G
Sbjct: 1 PLGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE---GSSGRQVTITG 57
Query: 90 TIDEILRAVDLVIDKLLTE 108
+ I A L+ +L +E
Sbjct: 58 SAASISLAQYLINARLSSE 76
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 45/75 (60%), Gaps = 5/75 (6%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
IR L+ G++IGK G ++ + +SGARI +S + + +RII ++G + I +
Sbjct: 5 IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----SPERIITLTGPTNAIFK 59
Query: 97 AVDLVIDKLLTELHA 111
A ++IDKL ++++
Sbjct: 60 AFAMIIDKLEEDINS 74
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
+RL++ GSIIGK G ++K ++S A I IS + +R++TLTG + +
Sbjct: 5 IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNSP-----ERIITLTGPTNAIFK 59
Query: 184 ALELILLKLSED 195
A +I+ KL ED
Sbjct: 60 AFAMIIDKLEED 71
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 266 EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQ 325
+ +G ++G+ G ++ I + SGARI +S+ + ER +T++GP +I A +MI+
Sbjct: 12 KEVGSIIGKKGESVKRIREESGARINISE-----GNSPERIITLTGPTNAIFKAFAMIID 66
Query: 326 KV 327
K+
Sbjct: 67 KL 68
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
IR L+ G++IGK G ++ + +SGARI +S + +RII ++G + I +
Sbjct: 5 IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----CPERIITLTGPTNAIFK 59
Query: 97 AVDLVIDKLLTELHA 111
A ++IDKL ++++
Sbjct: 60 AFAMIIDKLEEDINS 74
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
+RL++ GSIIGK G ++K ++S A R++ S +R++TLTG + +
Sbjct: 5 IRLLMHGKEVGSIIGKKGESVKRIREESGA-----RINISEGNCPERIITLTGPTNAIFK 59
Query: 184 ALELILLKLSED 195
A +I+ KL ED
Sbjct: 60 AFAMIIDKLEED 71
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 5/62 (8%)
Query: 266 EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQ 325
+ +G ++G+ G ++ I + SGARI +S+ ER +T++GP +I A +MI+
Sbjct: 12 KEVGSIIGKKGESVKRIREESGARINISE-----GNCPERIITLTGPTNAIFKAFAMIID 66
Query: 326 KV 327
K+
Sbjct: 67 KL 68
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQR 314
+T S + + ++ IG ++GR G I EI Q SGA+IK+++ G+++R+VTI+G
Sbjct: 3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANP---VEGSTDRQVTITGSAA 59
Query: 315 SIRTAESMI 323
SI A+ +I
Sbjct: 60 SISLAQYLI 68
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ 181
T L +PN G IIG+ GA I S A IKI+ + G DR VT+TG+
Sbjct: 5 TSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIA---NPVEGSTDRQVTITGSAASI 61
Query: 182 MRALELILLKLSEDT 196
A LI ++LS +T
Sbjct: 62 SLAQYLINVRLSSET 76
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAV 98
+ N L G +IG+ G+ IN+ + SGA+I+++ E G+TDR + I+G+ I A
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVE---GSTDRQVTITGSAASISLAQ 65
Query: 99 DLVIDKLLTE 108
L+ +L +E
Sbjct: 66 YLINVRLSSE 75
>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 = 6e-05, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 41 VSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDL 100
+ LAG++IGKGG I + +SGA I++ E G+ DRII I+GT D+I A L
Sbjct: 20 IPKDLAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNAQYL 76
Query: 101 V 101
+
Sbjct: 77 L 77
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
++ +P GSIIGK G IK +S A IKI D G DR++T+TGT D+ A
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 73
Query: 185 LELI 188
L+
Sbjct: 74 QYLL 77
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 269 GFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVA 328
G ++G+GG+ I +I SGA IK+ + G+ +R +TI+G Q I+ A+ ++ V
Sbjct: 26 GSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVK 82
Query: 329 YASDRLM 335
S +
Sbjct: 83 QYSGKFF 89
>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 = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 41 VSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDL 100
+ LAG++IGKGG I + +SGA I++ E G+ DRII I+GT D+I A L
Sbjct: 13 IPKDLAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNAQYL 69
Query: 101 V 101
+
Sbjct: 70 L 70
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
++ +P GSIIGK G IK +S A IKI D G DR++T+TGT D+ A
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 66
Query: 185 LELI 188
L+
Sbjct: 67 QYLL 70
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 269 GFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVA 328
G ++G+GG+ I +I SGA IK+ + G+ +R +TI+G Q I+ A+ ++ V
Sbjct: 19 GSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVK 75
Query: 329 YASDRLM 335
S +
Sbjct: 76 QYSGKFF 82
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
+L VP S G IIG+ G TI+S S A I + L RL+ ++GT E A
Sbjct: 18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-LLSRLIKISGTQKEVAAA 76
Query: 185 LELILLKLSED 195
LIL K+SED
Sbjct: 77 KHLILEKVSED 87
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGT--TDRIIMISGTI 91
P + + V G +IG+GG TI SGA+I + E GT R+I ISGT
Sbjct: 14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE---GTLLLSRLIKISGTQ 70
Query: 92 DEILRAVDLVIDKL 105
E+ A L+++K+
Sbjct: 71 KEVAAAKHLILEKV 84
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAE 320
+ V +G ++GRGG I I + SGA+I D+ + R + ISG Q+ + A+
Sbjct: 19 LSVPQRSVGRIIGRGGETIRSICKASGAKI-TCDKESEGTLLLSRLIKISGTQKEVAAAK 77
Query: 321 SMIMQKVA 328
+I++KV+
Sbjct: 78 HLILEKVS 85
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
IR L G++IGK G ++ + +SGARI +S + +RII ++G + I +
Sbjct: 7 IRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGN-----CPERIITLAGPTNAIFK 61
Query: 97 AVDLVIDKL 105
A +IDKL
Sbjct: 62 AFAXIIDKL 70
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
+RL+ GSIIGK G ++K ++S A I IS + +R++TL G + +
Sbjct: 7 IRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGN-----CPERIITLAGPTNAIFK 61
Query: 184 ALELILLKLSED 195
A I+ KL ED
Sbjct: 62 AFAXIIDKLEED 73
Score = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 266 EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQ 325
+ +G ++G+ G ++ + + SGARI +S+ ER +T++GP +I A + I+
Sbjct: 14 KEVGSIIGKKGESVKKXREESGARINISE-----GNCPERIITLAGPTNAIFKAFAXIID 68
Query: 326 KV 327
K+
Sbjct: 69 KL 70
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 263 VADEHIGFVVGRGGRNIMEISQISGARIKVS-DRGDFFSGTSERKVTISGPQRSIRTAES 321
V D +G ++GRGG I +I Q SG ++++S D G G ER V+++G S++ A+
Sbjct: 22 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSG----GLPERSVSLTGAPESVQKAKM 77
Query: 322 MI 323
M+
Sbjct: 78 ML 79
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAV 98
+ V + + G +IG+GG IN Q SG ++Q+S P +R + ++G + + +A
Sbjct: 20 YRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGAPESVQKA- 75
Query: 99 DLVIDKLLT 107
+++D +++
Sbjct: 76 KMMLDDIVS 84
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 128 VPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
VP+ G IIG+ G I DS ++IS GL +R V+LTG + +A
Sbjct: 22 VPDGMVGLIIGRGGEQINKIQQDSGCKVQIS---PDSGGLPERSVSLTGAPESVQKA 75
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 36/134 (26%), Positives = 64/134 (47%), Gaps = 12/134 (8%)
Query: 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEI 94
T ++ AG VIGKGG TI Q ++G ++ L + D+ + I G ++
Sbjct: 2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT-NVDKPLRIIGDPYKV 60
Query: 95 LRAVDLVIDKLLTELHAEDQA-----DDVGTKT--KLRLIVPNSSCGSIIGKAGATIKSF 147
+A ++V+D L DQ ++ G++ + + VP S G +IG++G IK
Sbjct: 61 QQACEMVMDI----LRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKI 116
Query: 148 MDDSQAVIKISRLD 161
+D+ I+ + D
Sbjct: 117 QNDAGVRIQFKQDD 130
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/123 (25%), Positives = 59/123 (47%), Gaps = 5/123 (4%)
Query: 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILR 96
++ + GA+IGK G I + A I+++ P + R+++I+G + +
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRMVIITGPPEAQFK 62
Query: 97 AVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK 156
A + KL E + ++V +T +R VP S+ G +IGK G T+ + + A +
Sbjct: 63 AQGRIYGKLKEE-NFFGPKEEVKLETHIR--VPASAAGRVIGKGGKTVNELQNLTAAEVV 119
Query: 157 ISR 159
+ R
Sbjct: 120 VPR 122
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
+++ +P + G+IIGK G IK + A IKI+ + + R+V +TG + Q +
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKV--RMVIITGPPEAQFK 62
Query: 184 ALELILLKLSEDTLY 198
A I KL E+ +
Sbjct: 63 AQGRIYGKLKEENFF 77
Score = 35.4 bits (80), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 4/52 (7%)
Query: 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIM 86
T+IR S AG VIGKGG T+N+ Q+ + A + + R P D++I+
Sbjct: 87 THIRVPAS--AAGRVIGKGGKTVNELQNLTAAEVVVPRDQT--PDENDQVIV 134
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101
LA ++IGKGG I + +SGA I++ E G+ DRII I+GT D+I A L+
Sbjct: 24 LARSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNAQYLL 77
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRA 184
++ +P SIIGK G IK +S A IKI D G DR++T+TGT D+ A
Sbjct: 17 QVTIPKDLARSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNA 73
Query: 185 LELI 188
L+
Sbjct: 74 QYLL 77
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 271 VVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA 330
++G+GG+ I +I SGA IK+ + G+ +R +TI+G Q I+ A+ ++ V
Sbjct: 28 IIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 84
Query: 331 SDRLM 335
S +
Sbjct: 85 SGKFF 89
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 263 VADEHIGFVVGRGGRNIMEISQISGARIKVS-DRGDFFSGTSERKVTISGPQRSIRTAES 321
V D +GF++GRGG I I Q SG +I+++ D G G ER ++G S+++A+
Sbjct: 21 VPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG----GLPERSCMLTGTPESVQSAKR 76
Query: 322 MIMQKV 327
++ Q V
Sbjct: 77 LLDQIV 82
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEIL--- 95
+ V + + G +IG+GG I+ Q +SG +IQ++ P +R M++GT + +
Sbjct: 19 YKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPESVQSAK 75
Query: 96 RAVDLVIDK 104
R +D +++K
Sbjct: 76 RLLDQIVEK 84
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 128 VPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL 187
VP+ G IIG+ G I +S I+I+ GL +R LTGT + A L
Sbjct: 21 VPDGMVGFIIGRGGEQISRIQQESGCKIQIA---PDSGGLPERSCMLTGTPESVQSAKRL 77
Query: 188 I 188
+
Sbjct: 78 L 78
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 36/69 (52%)
Query: 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRT 318
+T + G V+GRGG N+ I+Q +GA +++S + + + I G + I
Sbjct: 9 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDH 68
Query: 319 AESMIMQKV 327
A+ +I +K+
Sbjct: 69 AKQLIEEKI 77
Score = 32.7 bits (73), Expect = 0.28, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTD---RIIMISGTIDEIL 95
F + G VIG+GG + Q+GA +++SR P D ++ +I G+ +I
Sbjct: 11 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQ---LPPNGDPNFKLFIIRGSPQQID 67
Query: 96 RAVDLVIDKL 105
A L+ +K+
Sbjct: 68 HAKQLIEEKI 77
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 32/65 (49%)
Query: 128 VPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL 187
+P CG +IG+ G +K+ + A ++ISR N +L + G+ + A +L
Sbjct: 13 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQL 72
Query: 188 ILLKL 192
I K+
Sbjct: 73 IEEKI 77
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 46 AGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVID 103
AG VIGKGG TI Q ++G ++ + + G D+ + I+G ++ +A ++V++
Sbjct: 26 AGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTG-ADKPLRITGDPYKVQQAKEMVLE 82
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 126 LIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL-DHSYYGLNDRLVTLTGTLDEQMRA 184
+++P S G +IGK G TIK + +A +K+ + D D+ + +TG + +A
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQE--RAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQA 76
Query: 185 LELIL 189
E++L
Sbjct: 77 KEMVL 81
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 269 GFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQ 325
G V+G+GG I ++ + +G ++ + G +G +++ + I+G ++ A+ M+++
Sbjct: 27 GLVIGKGGETIKQLQERAGVKMVMIQDGPQNTG-ADKPLRITGDPYKVQQAKEMVLE 82
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 31.2 bits (69), Expect = 0.80, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 46 AGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL 105
AG VIGKGG TI Q ++G ++ L + D+ + I G ++ +A ++V+D L
Sbjct: 25 AGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPYKVQQACEMVMDIL 83
>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 = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 33/122 (27%), Positives = 45/122 (36%), Gaps = 34/122 (27%)
Query: 38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRA 97
+F+V L G IG GA IQ +R PG T A
Sbjct: 7 QFIVREDLXGLAIGT-----------HGANIQQARK---VPGVT---------------A 37
Query: 98 VDLVIDKLLTELHAEDQADDVGTKTKLRLI-----VPNSSCGSIIGKAGATIKSFMDDSQ 152
+DL D ++ EDQ ++ L VP + G +IGK G I+ +D S
Sbjct: 38 IDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSG 97
Query: 153 AV 154
V
Sbjct: 98 VV 99
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 260 TIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRG 296
TI + + I V+G GG+ I EI +GA++ ++D G
Sbjct: 573 TINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDG 609
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 260 TIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRG 296
TI + + I V+G GG+ I EI +GA++ ++D G
Sbjct: 573 TINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDG 609
>pdb|3ECY|A Chain A, Crystal Structural Analysis Of Drosophila Melanogaster
Dutpase
pdb|3ECY|B Chain B, Crystal Structural Analysis Of Drosophila Melanogaster
Dutpase
Length = 160
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179
KT L++ VP S G + ++G +K+F+D V+ D Y G ++ +D
Sbjct: 62 VKTDLQVQVPEGSYGRVAPRSGLAVKNFIDVGAGVV-----DEDYRGNLGVVLFNHSDVD 116
Query: 180 EQMRALELILLKLSEDTLYSQTMTV 204
+++ + I + E Y Q + V
Sbjct: 117 FEVKHGDRIAQFICERIFYPQLVMV 141
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 260 TIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRG 296
TI + + I V+G GG+ I EI +GA++ ++D G
Sbjct: 564 TINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDG 600
>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 = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL 105
G VIG+ G I Q+ +G RIQ + P ++I I G D A ++ D L
Sbjct: 23 GVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP---EKIAHIMGPPDRCEHAARIINDLL 78
>pdb|2HH3|A Chain A, Solution Structure Of The Third Kh Domain Of Ksrp
Length = 106
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL 105
G VIG+ G I Q+ +G RIQ + P ++I I G D A ++ D L
Sbjct: 23 GVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP---EKIAHIMGPPDRCEHAARIINDLL 78
>pdb|1CF2|P Chain P, Three-Dimensional Structure Of
D-Glyceraldehyde-3-Phosphate Dehydrogenase From The
Hyperthermophilic Archaeon Methanothermus Fervidus
pdb|1CF2|R Chain R, Three-Dimensional Structure Of
D-Glyceraldehyde-3-Phosphate Dehydrogenase From The
Hyperthermophilic Archaeon Methanothermus Fervidus
pdb|1CF2|O Chain O, Three-Dimensional Structure Of
D-Glyceraldehyde-3-Phosphate Dehydrogenase From The
Hyperthermophilic Archaeon Methanothermus Fervidus
pdb|1CF2|Q Chain Q, Three-Dimensional Structure Of
D-Glyceraldehyde-3-Phosphate Dehydrogenase From The
Hyperthermophilic Archaeon Methanothermus Fervidus
Length = 337
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 11/52 (21%)
Query: 59 DFQSQSGARIQLSRSHEFFPGTTDRI-------IMISGTIDEILRAVDLVID 103
DF+ AR+ L + ++ + +R+ I ++GT+D++L D+VID
Sbjct: 37 DFE----ARMALKKGYDLYVAIPERVKLFEKAGIEVAGTVDDMLDEADIVID 84
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
0.316 0.133 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,247,123
Number of Sequences: 62578
Number of extensions: 369586
Number of successful extensions: 938
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 796
Number of HSP's gapped (non-prelim): 113
length of query: 336
length of database: 14,973,337
effective HSP length: 99
effective length of query: 237
effective length of database: 8,778,115
effective search space: 2080413255
effective search space used: 2080413255
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)