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= 009023
(546 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 1e-04, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 5/69 (7%)
Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
GG +T ++ +P D G +IGKGGQ ++ IR E+GA I+I DE L D ++ I+
Sbjct: 10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGS---EDRIITIT 64
Query: 196 GEASVVKKA 204
G ++ A
Sbjct: 65 GTQDQIQNA 73
Score = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429
TT++ +P G +IGKGG I ++R + A+I+I + P SE D ++ I+G D
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSE-DRIITITGTQD 68
Query: 430 LAKDA 434
++A
Sbjct: 69 QIQNA 73
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 24/34 (70%)
Query: 65 VKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE 98
+KQ+R ++ + I+I E + GSE+R++T+ D+
Sbjct: 36 IKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 69
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 308 QIRQESGAAIKVDSSSTEGDDCLITVSSKE 337
QIR ESGA+IK+D +D +IT++ +
Sbjct: 38 QIRHESGASIKIDEPLEGSEDRIITITGTQ 67
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/151 (27%), Positives = 71/151 (47%), Gaps = 28/151 (18%)
Query: 65 VKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124
VK++R ++ ++I I E ER++T+ ++ A+FK +I
Sbjct: 27 VKKMREESGARINISEG--NCPERIITLAGPTN-----------------AIFKAFAMII 67
Query: 125 AEELRGDEDSDGGHQ-------VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILK 177
++L D S + VT +L+VP+ Q G +IGKGG ++ IR TGAQ+++
Sbjct: 68 -DKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG 126
Query: 178 DEHLPSCALRSDELVQISGEASVVKKALCQI 208
D LP+ R+ + I K +C +
Sbjct: 127 D-MLPNSTERAITIAGIPQSIIECVKQICVV 156
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 46/81 (56%), Gaps = 7/81 (8%)
Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199
+T +LL+ ++G +IGK G+ V+ +R E+GA+I I + + P + ++ ++G +
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAGPTN 57
Query: 200 VVKKALCQIASRLHDNPSRSQ 220
+ KA I +L ++ S S
Sbjct: 58 AIFKAFAMIIDKLEEDISSSM 78
Score = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%)
Query: 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405
T RL+VP S+ G LIGKGG I E+R T A +++
Sbjct: 89 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQV 124
Score = 28.5 bits (62), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 25/107 (23%), Positives = 50/107 (46%), Gaps = 11/107 (10%)
Query: 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427
++ T RLL+ +G +IGK G + +MR + A I I + N P + ++ ++G
Sbjct: 3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAGP 55
Query: 428 LDLAKDALIQVMTRLR----ANLFDREGAVSTFVPVLPYIPVSENGS 470
+ A ++ +L +++ + A V + +P S+ GS
Sbjct: 56 TNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGS 102
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 39/157 (24%), Positives = 77/157 (49%), Gaps = 12/157 (7%)
Query: 65 VKQLRIDTKSKIRIGET---VPGSEERVVTVYSASDETNAFED--GDKFVSPAQDALFKV 119
+ QL+ +T + I++ ++ PG+ ERV + + NA +K Q+
Sbjct: 28 IVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREXPQNV--AK 85
Query: 120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
+ V + + + D +QV K++VP+ G +IGKGG V+ I ++GA +++ +
Sbjct: 86 TEPVSILQPQTTVNPDRANQV--KIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQK- 142
Query: 180 HLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216
P + +V +SGE +KA+ I ++ ++P
Sbjct: 143 --PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP 177
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 28/43 (65%)
Query: 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
G Q K+L+PS G +IGKGGQ + ++ ETGA I++ K +
Sbjct: 3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSK 45
Score = 36.2 bits (82), Expect = 0.048, Method: Composition-based stats.
Identities = 38/177 (21%), Positives = 79/177 (44%), Gaps = 19/177 (10%)
Query: 283 EFSLRLVCPXXXXXXXXXXXXXXXXQIRQESGAAIKVDSSS-----TEGDDCLITVSSKE 337
++ L+++ P Q+++E+GA IK+ S T CLI + +
Sbjct: 5 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA 64
Query: 338 FFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT---------RLLVPTSRIGCLIGKG 388
+ + I +R P+ K E S L TT +++VP S G +IGKG
Sbjct: 65 L--NAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKG 122
Query: 389 GSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445
G+ + + + A +++ K P + + +V +SG+ + + A+ ++ +++ +
Sbjct: 123 GATVKAIXEQSGAWVQLSQK---PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 39/157 (24%), Positives = 77/157 (49%), Gaps = 12/157 (7%)
Query: 65 VKQLRIDTKSKIRIGET---VPGSEERVVTVYSASDETNAFED--GDKFVSPAQDALFKV 119
+ QL+ +T + I++ ++ PG+ ERV + + NA +K Q+
Sbjct: 28 IVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNV--AK 85
Query: 120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
+ V + + + D +QV K++VP+ G +IGKGG V+ I ++GA +++ +
Sbjct: 86 TEPVSILQPQTTVNPDRANQV--KIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQK- 142
Query: 180 HLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216
P + +V +SGE +KA+ I ++ ++P
Sbjct: 143 --PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP 177
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 28/43 (65%)
Query: 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
G Q K+L+PS G +IGKGGQ + ++ ETGA I++ K +
Sbjct: 3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSK 45
Score = 35.8 bits (81), Expect = 0.055, Method: Composition-based stats.
Identities = 38/177 (21%), Positives = 79/177 (44%), Gaps = 19/177 (10%)
Query: 283 EFSLRLVCPXXXXXXXXXXXXXXXXQIRQESGAAIKVDSSS-----TEGDDCLITVSSKE 337
++ L+++ P Q+++E+GA IK+ S T CLI + +
Sbjct: 5 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA 64
Query: 338 FFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT---------RLLVPTSRIGCLIGKG 388
+ + I +R P+ K E S L TT +++VP S G +IGKG
Sbjct: 65 L--NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKG 122
Query: 389 GSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445
G+ + + + A +++ K P + + +V +SG+ + + A+ ++ +++ +
Sbjct: 123 GATVKAIMEQSGAWVQLSQK---PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176
>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 = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE 197
H +T +LL+ ++G +IGK G+ V+ IR E+GA+I I S + ++ ++G
Sbjct: 1 HMLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI-------SEGNSPERIITLTGP 53
Query: 198 ASVVKKALCQIASRLHDNPSRS 219
+ + KA I +L ++ + S
Sbjct: 54 TNAIFKAFAMIIDKLEEDINSS 75
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG 196
G Q T +L +P++ IGC+IG+ G + IR +GAQI+I S V I+G
Sbjct: 3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN-----PVEGSSGRQVTITG 57
Query: 197 EASVVKKALCQIASRL 212
A+ + A I +RL
Sbjct: 58 SAASISLAQYLINARL 73
Score = 36.2 bits (82), Expect = 0.046, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 25/35 (71%)
Query: 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405
T L +P + IGC+IG+ G+ I E+R+++ A I+I
Sbjct: 7 THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI 41
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199
+T ++ +P D G +IGKGGQ ++ IR E+GA I+I DE L D ++ I+G
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGS---EDRIITITGTQD 61
Query: 200 VVKKA 204
++ A
Sbjct: 62 QIQNA 66
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429
TT++ +P G +IGKGG I ++R + A+I+I + P SE D ++ I+G D
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSE-DRIITITGTQD 61
Query: 430 LAKDA 434
++A
Sbjct: 62 QIQNA 66
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 24/34 (70%)
Query: 65 VKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE 98
+KQ+R ++ + I+I E + GSE+R++T+ D+
Sbjct: 29 IKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 62
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 308 QIRQESGAAIKVDSSSTEGDDCLITVSSKE 337
QIR ESGA+IK+D +D +IT++ +
Sbjct: 31 QIRHESGASIKIDEPLEGSEDRIITITGTQ 60
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195
GG +T ++ +P D +IGKGGQ ++ IR E+GA I+I DE L D ++ I+
Sbjct: 10 GGPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI--DEPLEGS---EDRIITIT 64
Query: 196 GEASVVKKA 204
G ++ A
Sbjct: 65 GTQDQIQNA 73
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 24/34 (70%)
Query: 65 VKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE 98
+KQ+R ++ + I+I E + GSE+R++T+ D+
Sbjct: 36 IKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 69
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429
TT++ +P +IGKGG I ++R + A+I+I + P SE D ++ I+G D
Sbjct: 14 ITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI----DEPLEGSE-DRIITITGTQD 68
Query: 430 LAKDA 434
++A
Sbjct: 69 QIQNA 73
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 308 QIRQESGAAIKVDSSSTEGDDCLITVSSKE 337
QIR ESGA+IK+D +D +IT++ +
Sbjct: 38 QIRHESGASIKIDEPLEGSEDRIITITGTQ 67
>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|B Chain B, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|C Chain C, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|D Chain D, Human Alpha Polyc Binding Protein Kh1
Length = 74
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 44/76 (57%), Gaps = 7/76 (9%)
Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199
+T +LL+ ++G +IGK G+ V+ IR E+GA+I I + +C R ++ ++G +
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG----NCPER---IITLTGPTN 55
Query: 200 VVKKALCQIASRLHDN 215
+ KA I +L ++
Sbjct: 56 AIFKAFAMIIDKLEED 71
>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 = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVK 202
+L +P+D IGC+IG+ G + IR +GAQI+I +D V I+G A+ +
Sbjct: 8 ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANP-----VEGSTDRQVTITGSAASIS 62
Query: 203 KALCQIASRL 212
A I RL
Sbjct: 63 LAQYLINVRL 72
Score = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANIRIL-PKENLPKIASEDDEMVQISGDLDLAK 432
L +P IGC+IG+ G+ I E+R+ + A I+I P E D V I+G A
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEG------STDRQVTITG--SAAS 60
Query: 433 DALIQVMTRLR 443
+L Q + +R
Sbjct: 61 ISLAQYLINVR 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 = 37.4 bits (85), Expect = 0.022, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 7/76 (9%)
Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199
+T +LL ++G +IGK G+ V+ R E+GA+I I + +C R ++ ++G +
Sbjct: 5 LTIRLLXHGKEVGSIIGKKGESVKKXREESGARINISEG----NCPER---IITLAGPTN 57
Query: 200 VVKKALCQIASRLHDN 215
+ KA I +L ++
Sbjct: 58 AIFKAFAXIIDKLEED 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 = 37.0 bits (84), Expect = 0.027, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 9/80 (11%)
Query: 348 EAVVRLQPRCSEKIERDSGL-----ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKAN 402
EA + Q R K++ ++ + T + VP S G +IGKGG + E++ LT A
Sbjct: 58 EAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAE 117
Query: 403 IRILPKENLPKIASEDDEMV 422
+ ++P++ P E+D+++
Sbjct: 118 V-VVPRDQTP---DENDQVI 133
Score = 33.5 bits (75), Expect = 0.35, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426
++ +P +G +IGK G I ++ R A+I+I P P+ MV I+G
Sbjct: 6 QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAP----PETPDSKVRMVIITG 55
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198
Q ++ +P+ +G +IGK GQ ++ + A I+I E P +R +V I+G
Sbjct: 2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE-TPDSKVR---MVIITGPP 57
Query: 199 SVVKKALCQIASRLHD 214
KA +I +L +
Sbjct: 58 EAQFKAQGRIYGKLKE 73
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179
VP+ G VIGKGG+ V +++ T A++ + +D+
Sbjct: 91 VPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQ 124
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 36.6 bits (83), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 45/90 (50%), Gaps = 15/90 (16%)
Query: 137 GHQ-----VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE-HLP--SCALR- 187
GHQ +T + VP +G +IG+GG+ + I+ E+G +I+I D LP SC L
Sbjct: 7 GHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTG 66
Query: 188 SDELVQISGEASVVKKALCQIASRLHDNPS 217
+ E VQ K+ L QI + PS
Sbjct: 67 TPESVQ------SAKRLLDQIVEKGRSGPS 90
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 35.8 bits (81), Expect = 0.070, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 48/78 (61%), Gaps = 5/78 (6%)
Query: 132 EDSDGGHQVTAK-LLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDE 190
++++GG T + +++P+ + G VIGKGG+ ++ ++ G ++ +++D S D+
Sbjct: 5 DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG---SQNTNVDK 61
Query: 191 LVQISGEASVVKKALCQI 208
++I G+ V++A C++
Sbjct: 62 PLRIIGDPYKVQQA-CEM 78
>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 = 35.4 bits (80), Expect = 0.075, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD-EHLPSCALRSDELVQISGEASVV 201
++ VP + +G ++GKGG+ + + TGA+I+I K E LP R V I+G +
Sbjct: 6 EMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRR---VTITGSPAAT 62
Query: 202 KKALCQIASRL 212
+ A I+ R+
Sbjct: 63 QAAQYLISQRV 73
Score = 32.0 bits (71), Expect = 0.81, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK-ENLP 412
+ VP + +G ++GKGG + E + LT A I+I K E LP
Sbjct: 7 MAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD-EHLPSCALRSDELVQISGEASVV 201
++ VP + +G ++GKGG+ + + TGA+I+I K E LP R V I+G +
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRR---VTITGSPAAT 62
Query: 202 KKALCQIASRL 212
+ A I+ R+
Sbjct: 63 QAAQYLISQRV 73
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK-ENLP 412
+ VP + +G ++GKGG + E + LT A I+I K E LP
Sbjct: 7 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46
>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 = 34.3 bits (77), Expect = 0.17, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 26/35 (74%)
Query: 144 LLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
+VP+ + G +IGKGG+ +++I ++GA+I + ++
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRN 142
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426
+VPT + G +IGKGG I + + + A I + + N P A + ++ I G
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRG 158
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVK 202
++++P+ + G VIGKGG+ ++ ++ G ++ +++D + A D+ ++I+G+ V+
Sbjct: 18 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA---DKPLRITGDPYKVQ 74
Query: 203 KALCQIASRLHDNPS 217
+A + + D S
Sbjct: 75 QAKEMVLELIRDQGS 89
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 43/69 (62%), Gaps = 6/69 (8%)
Query: 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD---LDL 430
+++P S+ G +IGKGG I +++ +A ++++ ++ P+ D + +I+GD +
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQE--RAGVKMVMIQDGPQNTGADKPL-RITGDPYKVQQ 75
Query: 431 AKDALIQVM 439
AK+ +++++
Sbjct: 76 AKEMVLELI 84
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 33.5 bits (75), Expect = 0.28, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD-EHLPSCALRSDELVQISGEASVV 201
++ VP + +G ++GKGG+ + + TG +I+I K E LP R V I+G +
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRK---VTITGTPAAT 62
Query: 202 KKALCQIASRL 212
+ A I R+
Sbjct: 63 QAAQYLITQRI 73
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK-ENLP 412
+ VP + +G ++GKGG + E + LT I+I K E LP
Sbjct: 7 IAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLP 46
>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 = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 24/33 (72%)
Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
+P+D+I VIG GG++++ I + TGA++ I D
Sbjct: 567 IPTDKIREVIGSGGKVIREIVATTGAKVDINDD 599
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 32.7 bits (73), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 24/33 (72%)
Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
+P+D+I VIG GG++++ I + TGA++ I D
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDINDD 608
>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 = 32.7 bits (73), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 24/33 (72%)
Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
+P+D+I VIG GG++++ I + TGA++ I D
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDINDD 608
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 32.7 bits (73), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
+P D+IG VIG Q++ I+ +TGA+I I D
Sbjct: 604 IPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD 636
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175
+P+ + G VIG+GG+ V+ I +TGA + I
Sbjct: 13 IPTHKCGLVIGRGGENVKAINQQTGAFVEI 42
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
+P D+IG VIG Q + I+ +TGA+I I D
Sbjct: 604 IPVDKIGEVIGPKRQXINQIQEDTGAEITIEDD 636
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE-HLPSCALRSDELVQISGEA 198
+T + VP +G +IG+GG+ + I+ ++G +++I D LP + V ++G
Sbjct: 16 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP------ERSVSLTGAP 69
Query: 199 SVVKKA 204
V+KA
Sbjct: 70 ESVQKA 75
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 28/109 (25%), Positives = 53/109 (48%), Gaps = 14/109 (12%)
Query: 113 QDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ 172
+ A+ K+H+ ++ EE + S VT ++++ + + G VIGK G + I TG
Sbjct: 74 EKAIRKIHE-IVPEEAKITNIS--FDDVTCEVIIEARKPGLVIGKYGSTSREIVKNTGWA 130
Query: 173 IRILKDEHLPSCALRSDELVQ-----ISGEASVVKKALCQIASRLHDNP 216
+IL+ + S E+++ + + KK L Q+ +R+H P
Sbjct: 131 PKILRTPPI------SSEIIERIRRTLRKNSKERKKILQQLGNRIHQKP 173
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 41/67 (61%), Gaps = 4/67 (5%)
Query: 143 KLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVK 202
++++P+ + G VIGKGG+ ++ ++ G ++ +++D S D+ ++I G+ V+
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG---SQNTNVDKPLRIIGDPYKVQ 61
Query: 203 KALCQIA 209
+A C++
Sbjct: 62 QA-CEMV 67
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG 196
V +L VP +G +IG+GG+ +++I +GA+I K+ L L++ISG
Sbjct: 15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE---GTLLLSRLIKISG 68
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 149 DQIGCVIGKGGQIVQNIRSETGAQIRILKD 178
D+I VIGKGG +++ + ETG I I D
Sbjct: 569 DKIKDVIGKGGSVIRALTEETGTTIEIEDD 598
>pdb|2CTL|A Chain A, Solution Structure Of The 13th Kh Type I Domain From Human
Vigilin
Length = 97
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 44/84 (52%), Gaps = 7/84 (8%)
Query: 362 ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEM 421
+ D L SF + V +IG+ G++IT++R NI+ K++ ++ +
Sbjct: 9 QEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD----GNQPQDQ 64
Query: 422 VQISG---DLDLAKDALIQVMTRL 442
+ I+G + + A+DA+++++ L
Sbjct: 65 ITITGYEKNTEAARDAILRIVGEL 88
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 0.134 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,173,410
Number of Sequences: 62578
Number of extensions: 487931
Number of successful extensions: 1112
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1030
Number of HSP's gapped (non-prelim): 89
length of query: 546
length of database: 14,973,337
effective HSP length: 104
effective length of query: 442
effective length of database: 8,465,225
effective search space: 3741629450
effective search space used: 3741629450
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: 54 (25.4 bits)