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= 022837
(291 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
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 111 bits (278), 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
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 75.5 bits (184), Expect = 4e-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 = 46.6 bits (109), Expect = 2e-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 = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183
+RL++ GSIIGK G ++K ++S A R++ S +R++TL G + +
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGA-----RINISEGNCPERIITLAGPTNAIFK 61
Query: 184 ALELILLKLSEDTLYSQT 201
A +I+ KL ED S T
Sbjct: 62 AFAMIIDKLEEDISSSMT 79
>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 = 56.6 bits (135), Expect = 2e-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 = 36.6 bits (83), Expect = 0.017, 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|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 = 56.6 bits (135), Expect = 2e-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 = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE 180
K + + VP + G+I+GK G T+ + + + A I+IS+ G +R VT+TG+
Sbjct: 2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61
Query: 181 QMRALELILLKLSEDTLYSQ 200
A LI S+ Y Q
Sbjct: 62 TQAAQYLI----SQRVTYEQ 77
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 56.6 bits (135), Expect = 2e-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 = 35.8 bits (81), Expect = 0.026, 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 = 56.6 bits (135), Expect = 2e-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
>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 = 48.5 bits (114), Expect = 4e-06, Method: Composition-based stats.
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 = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
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
>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 = 48.1 bits (113), Expect = 6e-06, Method: Composition-based stats.
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 = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
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 IRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-----CPERIITLTGPTNAIFK 59
Query: 184 ALELILLKLSED 195
A +I+ KL ED
Sbjct: 60 AFAMIIDKLEED 71
>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 = 45.4 bits (106), Expect = 3e-05, 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 = 40.8 bits (94), Expect = 9e-04, 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
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 3/53 (5%)
Query: 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRA 97
LAG++IGKGG I + +SGA I++ E G+ DRII I+GT D+I A
Sbjct: 24 LAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNA 73
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 42/89 (47%), Gaps = 16/89 (17%)
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 LELILLKLSEDTLYSQTMTVPYTYAGVFF 213
L+ + + Y+G FF
Sbjct: 74 QYLLQNSVKQ-------------YSGKFF 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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 3/53 (5%)
Query: 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRA 97
LAG++IGKGG I + +SGA I++ E G+ DRII I+GT D+I A
Sbjct: 17 LAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNA 66
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 42/89 (47%), Gaps = 16/89 (17%)
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 LELILLKLSEDTLYSQTMTVPYTYAGVFF 213
L+ + + Y+G FF
Sbjct: 67 QYLLQNSVKQ-------------YSGKFF 82
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 44.7 bits (104), Expect = 6e-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 = 41.2 bits (95), 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
>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|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRA 97
LA ++IGKGG I + +SGA I++ E G+ DRII I+GT D+I A
Sbjct: 24 LARSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNA 73
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 41/89 (46%), Gaps = 16/89 (17%)
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 LELILLKLSEDTLYSQTMTVPYTYAGVFF 213
L+ + + Y+G FF
Sbjct: 74 QYLLQNSVKQ-------------YSGKFF 89
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 41.2 bits (95), Expect = 7e-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 = 38.1 bits (87), 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 = 0.035, 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|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 = 41.2 bits (95), Expect = 8e-04, 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|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 39.7 bits (91), Expect = 0.002, 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 = 0.005, 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|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 37.4 bits (85), Expect = 0.010, 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 = 28.5 bits (62), Expect = 5.2, 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|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 37.4 bits (85), Expect = 0.010, 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 = 32.7 bits (73), Expect = 0.27, 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|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 34.7 bits (78), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 34/71 (47%)
Query: 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQM 182
++ +P CG +IG+ G +K+ + A ++ISR N +L + G+ +
Sbjct: 8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQID 67
Query: 183 RALELILLKLS 193
A +LI K+
Sbjct: 68 HAKQLIEEKIE 78
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 46 AGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTD---RIIMISGTIDEILRAVDLVI 102
G VIG+GG + Q+GA +++SR P D ++ +I G+ +I A L+
Sbjct: 18 CGLVIGRGGENVKAINQQTGAFVEISRQ---LPPNGDPNFKLFIIRGSPQQIDHAKQLIE 74
Query: 103 DKL 105
+K+
Sbjct: 75 EKI 77
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 32.3 bits (72), Expect = 0.32, 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|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 31.6 bits (70), Expect = 0.55, Method: Composition-based stats.
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
>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 = 30.8 bits (68), Expect = 0.98, 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|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|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 = 2.7, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL 106
G VIG+ G I Q+ +G RIQ + P ++I I G D A +I+ LL
Sbjct: 23 GVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP---EKIAHIMGPPDRCEHAA-RIINDLL 78
Query: 107 TELHA 111
L +
Sbjct: 79 QSLRS 83
>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 = 2.7, 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
>pdb|3IRV|A Chain A, Crystal Structure Of Cysteine Hydrolase Pspph_2384 From
Pseudomonas Syringae Pv. Phaseolicola 1448a
Length = 233
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 251 NKVLLPWPLNPVGMLLIILIAQPIICHFSLSIY 283
+K L+ WP+NP+ +I++ Q + C + ++Y
Sbjct: 10 SKPLVRWPINPLRTAVIVVDMQKVFCEPTGALY 42
>pdb|2HH3|A Chain A, Solution Structure Of The Third Kh Domain Of Ksrp
Length = 106
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL 106
G VIG+ G I Q+ +G RIQ + P ++I I G D A +I+ LL
Sbjct: 23 GVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP---EKIAHIMGPPDRCEHAA-RIINDLL 78
Query: 107 TELHA 111
L +
Sbjct: 79 QSLRS 83
>pdb|3CB4|D Chain D, The Crystal Structure Of Lepa
pdb|3CB4|A Chain A, The Crystal Structure Of Lepa
pdb|3CB4|B Chain B, The Crystal Structure Of Lepa
pdb|3CB4|C Chain C, The Crystal Structure Of Lepa
pdb|3CB4|E Chain E, The Crystal Structure Of Lepa
pdb|3CB4|F Chain F, The Crystal Structure Of Lepa
Length = 599
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 157 ISRLDHSYYGLNDRLVTLTGTL-DEQMRALELILLKLSED---TLYSQTMTVPY 206
I+ +DH L+DR++ + G L D +M A L + L + T+ +Q++T+ Y
Sbjct: 10 IAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDY 63
>pdb|3KVO|A Chain A, Crystal Structure Of The Catalytic Domain Of Human
Hydroxysteroid Dehydrogenase Like 2 (Hsdl2)
pdb|3KVO|B Chain B, Crystal Structure Of The Catalytic Domain Of Human
Hydroxysteroid Dehydrogenase Like 2 (Hsdl2)
Length = 346
Score = 28.1 bits (61), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 135 SIIGKAGATIKSFMDDSQAVIKISRLDHSYYGL-----NDRLVTLTGTLDEQMRALELIL 189
++ GKA I D+ Q + + + G+ N ++LT TLD + L+L++
Sbjct: 98 AVGGKALPCIVDVRDEQQISAAVEKAIKKFGGIDILVNNASAISLTNTLDTPTKRLDLMM 157
Query: 190 LKLSEDTLYSQTMTVPY 206
+ T + +PY
Sbjct: 158 NVNTRGTYLASKACIPY 174
>pdb|3DEG|C Chain C, Complex Of Elongating Escherichia Coli 70s Ribosome And
Ef4(Lepa)- Gmppnp
Length = 545
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 157 ISRLDHSYYGLNDRLVTLTGTL-DEQMRALELILLKLSED---TLYSQTMTVPY 206
I+ +DH L+DR++ + G L D +M A L + L + T+ +Q++T+ Y
Sbjct: 10 IAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDY 63
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
0.319 0.136 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,230,934
Number of Sequences: 62578
Number of extensions: 322466
Number of successful extensions: 834
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 747
Number of HSP's gapped (non-prelim): 61
length of query: 291
length of database: 14,973,337
effective HSP length: 98
effective length of query: 193
effective length of database: 8,840,693
effective search space: 1706253749
effective search space used: 1706253749
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)