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= psy11929
(433 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 = 126 bits (317), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 71/185 (38%), Positives = 107/185 (57%), Gaps = 27/185 (14%)
Query: 11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIXXXXXXX 70
++ +T+R L H E+ +IG G V+++R+ESGA+I+I++G CP+RI
Sbjct: 1 KNVTLTIRLLMHG----KEVGSIIGKKGESVKKMREESGARINISEGNCPERIITL---- 52
Query: 71 XXXXXXXXXXGYPGHTLWVTSVDNVCTAYNFMCRSLE-DYHINRNRMENCSPQPLQLKLV 129
P + ++ A+ + LE D + S P+ L+LV
Sbjct: 53 ----------AGPTNAIF--------KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLV 94
Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQIC 189
+PA+ CGSLIGKGGCKIK+IR+ +GA VQVA DMLP STER +T+ G P +I + + QIC
Sbjct: 95 VPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQIC 154
Query: 190 LVLIE 194
+V++E
Sbjct: 155 VVMLE 159
Score = 29.3 bits (64), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 300 GCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAV--SLAQYLINMCIELQ 357
G +IGK G + ++R+ SGA+INI G +++ + G A+ + A + + ++
Sbjct: 17 GSIIGKKGESVKKMREESGARINISEGN-CPERIITLAGPTNAIFKAFAMIIDKLEEDIS 75
Query: 358 KNNTTNTSDNPEPADLDAAISAFMTASV 385
+ T +T+ + P L + A S+
Sbjct: 76 SSMTNSTAASRPPVTLRLVVPASQCGSL 103
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/63 (46%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYL 349
E+ + +D+ GC+IG+ G+++ EIRQ SGAQI I E S + I G ++SLAQYL
Sbjct: 8 ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLAQYL 67
Query: 350 INM 352
IN+
Sbjct: 68 INV 70
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
+L IP G +IG+ G KI +IR SGA +++A + + ST+R VT+ G+ +IS A Y
Sbjct: 8 ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIA-NPVEGSTDRQVTITGSAASISLAQY 66
Query: 187 QICLVL 192
I + L
Sbjct: 67 LINVRL 72
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYL 349
E+ + +++ GC+IG+ G+ + EIRQ+SGAQI I E S + I G ++SLAQYL
Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYL 68
Query: 350 INMCIELQK 358
IN + +K
Sbjct: 69 INARLSSEK 77
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
+L IP G +IG+ G I +IR +SGA +++A + + S+ R VT+ G+ +IS A Y
Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIA-NPVEGSSGRQVTITGSAASISLAQY 67
Query: 187 QI 188
I
Sbjct: 68 LI 69
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 46/169 (27%), Positives = 75/169 (44%), Gaps = 36/169 (21%)
Query: 32 CLIGPGGCIVRRLRKESGAKISITDGACPDRIXXXXXXXXXXXXXXXXXGYPGHTLWVTS 91
+IG GG + +L+KE+GA I ++ YPG T V
Sbjct: 19 SIIGKGGQTIVQLQKETGATIKLSK---------------------SKDFYPGTTERVCL 57
Query: 92 VDNVCTAYN----FMCRSLEDYHINRNRMENCS---PQPL-------QLKLVIPATHCGS 137
+ A N F+ + + N + E S PQ Q+K+++P + G
Sbjct: 58 IQGTIEALNAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGL 117
Query: 138 LIGKGGCKIKDIRDLSGANVQVASDMLPMSTE-RIVTVHGNPDTISQAI 185
+IGKGG +K I + SGA VQ++ ++ + R+VTV G P+ +A+
Sbjct: 118 IIGKGGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAV 166
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 2/53 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQV--ASDMLPMSTERIVTVHG 176
LK++IP+ GS+IGKGG I ++ +GA +++ + D P +TER+ + G
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG 60
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 30/142 (21%), Positives = 59/142 (41%), Gaps = 18/142 (12%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLA 346
++++ AG +IGK G ++++++ +GA I + + + +++ IQG EA++
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 347 QYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGL 406
I I N T EP + + N I P G ++ GG
Sbjct: 69 HGFIAEKIREXPQNVAKT----EPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGG- 123
Query: 407 SELLANIAASNVKSTVQTTGAY 428
+ VK+ + +GA+
Sbjct: 124 ---------ATVKAIXEQSGAW 136
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 46/169 (27%), Positives = 75/169 (44%), Gaps = 36/169 (21%)
Query: 32 CLIGPGGCIVRRLRKESGAKISITDGACPDRIXXXXXXXXXXXXXXXXXGYPGHTLWVTS 91
+IG GG + +L+KE+GA I ++ YPG T V
Sbjct: 19 SIIGKGGQTIVQLQKETGATIKLSKSK---------------------DFYPGTTERVCL 57
Query: 92 VDNVCTAYN----FMCRSLEDYHINRNRMENCS---PQPL-------QLKLVIPATHCGS 137
+ A N F+ + + N + E S PQ Q+K+++P + G
Sbjct: 58 IQGTIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGL 117
Query: 138 LIGKGGCKIKDIRDLSGANVQVASDMLPMSTE-RIVTVHGNPDTISQAI 185
+IGKGG +K I + SGA VQ++ ++ + R+VTV G P+ +A+
Sbjct: 118 IIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAV 166
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 2/53 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQV--ASDMLPMSTERIVTVHG 176
LK++IP+ GS+IGKGG I ++ +GA +++ + D P +TER+ + G
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG 60
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 30/142 (21%), Positives = 60/142 (42%), Gaps = 18/142 (12%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLA 346
++++ AG +IGK G ++++++ +GA I + + + +++ IQG EA++
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 347 QYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGL 406
I I N T EP + + N I P G ++ GG
Sbjct: 69 HGFIAEKIREMPQNVAKT----EPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGG- 123
Query: 407 SELLANIAASNVKSTVQTTGAY 428
+ VK+ ++ +GA+
Sbjct: 124 ---------ATVKAIMEQSGAW 136
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 282 DTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQ 340
D G + T++ + D+AG +IGK G R+ +IR SGA I I E S ++ I G Q
Sbjct: 8 DLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 67
Query: 341 EAVSLAQYLINMCIE 355
+ + AQYL+ ++
Sbjct: 68 DQIQNAQYLLQNSVK 82
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
++ IP GS+IGKGG +IK IR SGA++++ + L S +RI+T+ G D I A Y
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNAQY 75
>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 = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
++ IP GS+IGKGG +IK IR SGA++++ + L S +RI+T+ G D I A Y
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNAQY 68
Score = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLA 346
+ T++ + D+AG +IGK G R+ +IR SGA I I E S ++ I G Q+ + A
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 66
Query: 347 QYLINMCIE 355
QYL+ ++
Sbjct: 67 QYLLQNSVK 75
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 282 DTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQ 340
D G + T++ + D+A +IGK G R+ +IR SGA I I E S ++ I G Q
Sbjct: 8 DLGGPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 67
Query: 341 EAVSLAQYLINMCIE 355
+ + AQYL+ ++
Sbjct: 68 DQIQNAQYLLQNSVK 82
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
++ IP S+IGKGG +IK IR SGA++++ + L S +RI+T+ G D I A Y
Sbjct: 17 QVTIPKDLARSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNAQY 75
>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 = 1e-05, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 35/50 (70%), Gaps = 4/50 (8%)
Query: 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRI 63
++T+R L H E+ +IG G V+R+R+ESGA+I+I++G CP+RI
Sbjct: 2 ILTIRLLMHGK----EVGSIIGKKGESVKRIREESGARINISEGNCPERI 47
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQ 183
L ++L++ GS+IGK G +K IR+ SGA + ++ P ERI+T+ G + I +
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCP---ERIITLTGPTNAIFK 59
Query: 184 AIYQI 188
A I
Sbjct: 60 AFAMI 64
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 300 GCVIGKAGSRLLEIRQISGAQINIHTG 326
G +IGK G + IR+ SGA+INI G
Sbjct: 15 GSIIGKKGESVKRIREESGARINISEG 41
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/50 (42%), Positives = 34/50 (68%), Gaps = 4/50 (8%)
Query: 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRI 63
++T+R L H E+ +IG G V+R+R+ESGA+I+I++G P+RI
Sbjct: 2 MLTIRLLMHG----KEVGSIIGKKGESVKRIREESGARINISEGNSPERI 47
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQ 183
L ++L++ GS+IGK G +K IR+ SGA + ++ P ERI+T+ G + I +
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNSP---ERIITLTGPTNAIFK 59
Query: 184 AIYQI 188
A I
Sbjct: 60 AFAMI 64
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 300 GCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLI 350
G +IGK G + IR+ SGA+INI G S +++ + G A+ A +I
Sbjct: 15 GSIIGKKGESVKRIREESGARINISEGN-SPERIITLTGPTNAIFKAFAMI 64
>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 = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 35/53 (66%), Gaps = 4/53 (7%)
Query: 11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRI 63
++ +T+R L H E+ +IG G V++ R+ESGA+I+I++G CP+RI
Sbjct: 1 KNVTLTIRLLXHG----KEVGSIIGKKGESVKKXREESGARINISEGNCPERI 49
Score = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQ 183
L ++L+ GS+IGK G +K R+ SGA + ++ P ERI+T+ G + I +
Sbjct: 5 LTIRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGNCP---ERIITLAGPTNAIFK 61
Query: 184 AIYQI 188
A I
Sbjct: 62 AFAXI 66
Score = 28.5 bits (62), Expect = 7.9, Method: Composition-based stats.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 300 GCVIGKAGSRLLEIRQISGAQINIHTG 326
G +IGK G + + R+ SGA+INI G
Sbjct: 17 GSIIGKKGESVKKXREESGARINISEG 43
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPMSTERIVTVHGNPDTISQ 183
+++ +P G+++GKGG + + ++L+GA +Q++ + LP + R VT+ G+P
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 184 AIYQI 188
A Y I
Sbjct: 65 AQYLI 69
Score = 38.5 bits (88), Expect = 0.008, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLA 346
E+ + +++ G ++GK G L+E ++++GA+I I E + + I G A A
Sbjct: 6 EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65
Query: 347 QYLIN 351
QYLI+
Sbjct: 66 QYLIS 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 = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPMSTERIVTVHGNPDTISQ 183
+++ +P G+++GKGG + + ++L+GA +Q++ + LP + R VT+ G+P
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 184 AIYQI 188
A Y I
Sbjct: 65 AQYLI 69
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLA 346
EI + +++ G ++GK G L+E ++++GA+I I E + + I G A A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65
Query: 347 QYLIN 351
QYLI+
Sbjct: 66 QYLIS 70
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPMSTERIVTVHGNPDTISQ 183
+++ +P G+++GKGG + + ++L+G +Q++ + LP + R VT+ G P
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQA 64
Query: 184 AIYQI 188
A Y I
Sbjct: 65 AQYLI 69
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLA 346
EI + +++ G ++GK G L+E ++++G +I I E + + I G A A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 347 QYLINMCI 354
QYLI I
Sbjct: 66 QYLITQRI 73
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
+++ IPA G++IGK G IK + + A++++A P S R+V + G P+ +A
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKA 63
Score = 37.4 bits (85), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIV 172
L+ + +PA+ G +IGKGG + ++++L+ A V V D P ++++
Sbjct: 85 LETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVI 133
>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 = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTE--RIVTVHGNPDTIS 182
+ ++P G +IGKGG IK I SGA +++ + P + ++ T+ G P I
Sbjct: 105 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 164
Query: 183 QA 184
A
Sbjct: 165 YA 166
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH----TGTESHKKMFHIQGCQEAVS 344
E ++ G +IGK G + I Q SGA+I + + + K+F I+G + +
Sbjct: 105 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 164
Query: 345 LAQYLINMCI 354
A+ LI I
Sbjct: 165 YARQLIEEKI 174
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 36.6 bits (83), Expect = 0.027, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTE--RIVTVHGNPDTIS 182
++ IP CG +IG+GG +K I +GA V+++ + P ++ + G+P I
Sbjct: 8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQID 67
Query: 183 QA 184
A
Sbjct: 68 HA 69
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 46/87 (52%), Gaps = 5/87 (5%)
Query: 109 YHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD-MLPMS 167
+H N N +N + Q +++IPA G +IGKGG IK +++ +G + + D +
Sbjct: 3 FHDNANGGQNGTVQ----EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTN 58
Query: 168 TERIVTVHGNPDTISQAIYQICLVLIE 194
++ + + G+P + QA + +L E
Sbjct: 59 VDKPLRIIGDPYKVQQACEMVMDILRE 85
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 35.0 bits (79), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 5/57 (8%)
Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM--LPMSTERIVTVHGNPDTISQA 184
+P G +IG+GG +I I+ SG VQ++ D LP ER V++ G P+++ +A
Sbjct: 22 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGAPESVQKA 75
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMST--ERIVTVHGNPDTISQA 184
+++IPA+ G +IGKGG IK +++ +G + + D P +T ++ + + G+P + QA
Sbjct: 18 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG-PQNTGADKPLRITGDPYKVQQA 76
Query: 185 IYQICLVLI 193
++ L LI
Sbjct: 77 -KEMVLELI 84
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM--LPMSTERIVTVHGNPDTISQA 184
+P G +IG+GG +I I+ SG +Q+A D LP ER + G P+++ A
Sbjct: 21 VPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPESVQSA 74
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD-MLPMSTERIVTVHGNPDTISQAI 185
+++IPA G +IGKGG IK +++ +G + + D + ++ + + G+P + QA
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQAC 64
Query: 186 YQICLVLIE 194
+ +L E
Sbjct: 65 EMVMDILRE 73
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITD 56
+N ++I +IG GG ++R L +E+G I I D
Sbjct: 565 KINPDKIKDVIGKGGSVIRALTEETGTTIEIED 597
>pdb|3FIM|B Chain B, Crystal Structure Of Aryl-Alcohol-Oxidase From Pleurotus
Eryingii
Length = 566
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 197 LQVVKGAVIPYEPKTMNAGPVILSGGQAYTL 227
L++V G+++P+ P GP+ L G Q L
Sbjct: 531 LRIVDGSILPFAPNAHTQGPIYLVGKQGADL 561
>pdb|2CTE|A Chain A, Solution Structure Of The 1st Kh Type I Domain From Human
Vigilin
Length = 94
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 128 LVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQ 187
+ IP H +IGK G K++D+ + +Q+ P + + G + I +A ++
Sbjct: 21 VAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR---PDDPSNQIKITGTKEGIEKARHE 77
Query: 188 ICLVLIE 194
+ L+ E
Sbjct: 78 VLLISAE 84
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANV---QVASDMLPMSTERIVTVHGNPD 179
P+ +L +P G +IG+GG I+ I SGA + + + L +S R++ + G
Sbjct: 14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS--RLIKISGTQK 71
Query: 180 TISQAIYQI 188
++ A + I
Sbjct: 72 EVAAAKHLI 80
>pdb|3EN0|A Chain A, The Structure Of Cyanophycinase
pdb|3EN0|B Chain B, The Structure Of Cyanophycinase
pdb|3EN0|C Chain C, The Structure Of Cyanophycinase
Length = 291
Score = 28.5 bits (62), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 33/85 (38%), Gaps = 16/85 (18%)
Query: 108 DYHI-NRNRMENC----SPQPLQLKLVIPATHCG--------SLIGKGGCKIKDIRDLSG 154
D H NRNRM S P L L I C +IG+G D RD+S
Sbjct: 192 DQHFHNRNRMARLLSAISTHPELLGLGIDEDTCAMFERDGSVKVIGQGTVSFVDARDMSY 251
Query: 155 ANVQVASDMLPMSTERI---VTVHG 176
N + P+S + + VHG
Sbjct: 252 TNAALVGANAPLSLHNLRLNILVHG 276
>pdb|1VIG|A Chain A, Nmr Study Of Vigilin, Repeat 6, 40 Structures
pdb|1VIH|A Chain A, Nmr Study Of Vigilin, Repeat 6, Minimized Average
Structure
Length = 71
Score = 28.1 bits (61), Expect = 9.5, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 138 LIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
LIGK G I I+D +V++ D ++ + G+P + QA
Sbjct: 19 LIGKSGANINRIKDQYKVSVRIPPD---SEKSNLIRIEGDPQGVQQA 62
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
0.317 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,214,266
Number of Sequences: 62578
Number of extensions: 470102
Number of successful extensions: 1040
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 952
Number of HSP's gapped (non-prelim): 80
length of query: 433
length of database: 14,973,337
effective HSP length: 102
effective length of query: 331
effective length of database: 8,590,381
effective search space: 2843416111
effective search space used: 2843416111
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)