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= 045766
(663 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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 41/157 (26%), Positives = 81/157 (51%), Gaps = 11/157 (7%)
Query: 317 LTFRLLCHDERXXXXXXXXXXXXRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRI 376
LT RLL H + + +++E+G I + E +R+I ++GP + +
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFK- 61
Query: 377 SAPQDAVLRVQTRIARAIPDNREQT---VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGA 433
A + +++ I+ ++ ++ + V RL+V ++Q G L+GKGG I E+R+ +GA
Sbjct: 62 -AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGA 120
Query: 434 YIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQI 470
+++ G D +P + E + I G +++ E + QI
Sbjct: 121 QVQVAG-DMLP---NSTERAITIAGIPQSIIECVKQI 153
Score = 36.6 bits (83), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 153 TSKVQKALLLVFERMVEVEPETEVADQENTKSSK--FVLRLLVLSTQVGCLLGKGGCVIK 210
T+ + KA ++ +++ E + + +T +S+ LRL+V ++Q G L+GKGGC IK
Sbjct: 56 TNAIFKAFAMIIDKL---EEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIK 112
Query: 211 QI 212
+I
Sbjct: 113 EI 114
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 30/110 (27%), Positives = 47/110 (42%), Gaps = 10/110 (9%)
Query: 401 TVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEF 460
T+ RLL+ ++G ++GK G + +MR+ SGA I I + P E ++ + G
Sbjct: 4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAGPT 56
Query: 461 EAVQEALFQITTRLRHHFFRDAFPSINRPLNPTFLDQVSPFP---SFIGR 507
A+ +A I +L S P L V P S IG+
Sbjct: 57 NAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGK 106
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 33/58 (56%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFVMSET 660
I G GA + +IRQ S A+I I +P G+T+ + I+G+ AQ LI + SET
Sbjct: 19 IIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSET 76
Score = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 398 REQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLIN 457
+ QT L + ++ IGC++G+ G+ I E+R+ SGA I+I P S + +V I
Sbjct: 1 KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIAN----PVEGSTDRQVT-IT 55
Query: 458 GEFEAVQEALFQITTRL 474
G ++ A + I RL
Sbjct: 56 GSAASISLAQYLINVRL 72
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 32/54 (59%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFV 656
I G+ G +KQIR S A I I +P G+ + +I I+GT +Q AQ L+Q V
Sbjct: 28 IIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSV 81
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 38/63 (60%)
Query: 46 IMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETS 105
I +V P +IGK G+ + QI ++G +I+++E + GS++R++ I + ++ + +
Sbjct: 14 ITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 73
Query: 106 ENL 108
+ L
Sbjct: 74 QYL 76
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 340 RSLKQETGCDIKVMEAVSGTEDRLIVISG 368
+ ++ E+G IK+ E + G+EDR+I I+G
Sbjct: 37 KQIRHESGASIKIDEPLEGSEDRIITITG 65
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFE 461
+ T++ + + ++GKGG I ++R SGA I+I D+ P SE + ++ I G +
Sbjct: 14 ITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI---DE-PLEGSE-DRIITITGTQD 68
Query: 462 AVQEALFQITTRLRHH---FF 479
+Q A + + ++ + FF
Sbjct: 69 QIQNAQYLLQNSVKQYSGKFF 89
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 32/54 (59%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFV 656
I G+ G +KQIR S A I I +P G+ + +I I+GT +Q AQ L+Q V
Sbjct: 28 IIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSV 81
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 38/63 (60%)
Query: 46 IMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETS 105
I +V P +IGK G+ + QI ++G +I+++E + GS++R++ I + ++ + +
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 73
Query: 106 ENL 108
+ L
Sbjct: 74 QYL 76
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 8/81 (9%)
Query: 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFE 461
+ T++ + + G ++GKGG I ++R SGA I+I D+ P SE + ++ I G +
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DE-PLEGSE-DRIITITGTQD 68
Query: 462 AVQEALFQITTRLRHH---FF 479
+Q A + + ++ + FF
Sbjct: 69 QIQNAQYLLQNSVKQYSGKFF 89
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 340 RSLKQETGCDIKVMEAVSGTEDRLIVISG 368
+ ++ E+G IK+ E + G+EDR+I I+G
Sbjct: 37 KQIRHESGASIKIDEPLEGSEDRIITITG 65
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 20/77 (25%)
Query: 193 VLSTQV-------GCLLGKGGCVIKQIDKLPTCALASDE--------VVQITGEVDTVRK 237
+++TQV G ++GKGG IKQI ++ DE ++ ITG D ++
Sbjct: 13 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQN 72
Query: 238 ALKLISHQLLDNSPRDH 254
A LL NS + +
Sbjct: 73 A-----QYLLQNSVKQY 84
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 33/57 (57%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFVMSE 659
I G GA + +IRQ+S A+I I +P G++ + I+G+ AQ LI A + SE
Sbjct: 20 IIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE 76
Score = 38.1 bits (87), Expect = 0.016, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 406 LLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQE 465
L + +N IGC++G+ G+ I E+R++SGA I+I P S +V I G ++
Sbjct: 10 LTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN----PVEGSSGRQVT-ITGSAASISL 64
Query: 466 ALFQITTRL 474
A + I RL
Sbjct: 65 AQYLINARL 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 = 0.004, Method: Compositional matrix adjust.
Identities = 35/119 (29%), Positives = 61/119 (51%), Gaps = 16/119 (13%)
Query: 364 IVISGPAHPDDR-----ISAPQDAVLRVQTRIARAIPD------NREQTVMTRLLVASNQ 412
I I+ P PD + I+ P +A + Q RI + + E + T + V ++
Sbjct: 36 IKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASA 95
Query: 413 IGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVL-INGEFEAVQEALFQI 470
G ++GKGG + E++ L+ A + ++ +DQ P EN++V++ I G F A Q A +I
Sbjct: 96 AGRVIGKGGKTVNELQNLTAAEV-VVPRDQTP---DENDQVIVKIIGHFYASQMAQRKI 150
>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 = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 32/54 (59%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFV 656
I G+ G +KQIR S A I I +P G+ + +I I+GT +Q AQ L+Q V
Sbjct: 21 IIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSV 74
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 38/63 (60%)
Query: 46 IMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETS 105
I +V P +IGK G+ + QI ++G +I+++E + GS++R++ I + ++ + +
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 66
Query: 106 ENL 108
+ L
Sbjct: 67 QYL 69
Score = 33.1 bits (74), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 8/81 (9%)
Query: 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFE 461
+ T++ + + G ++GKGG I ++R SGA I+I D+ P SE + ++ I G +
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DE-PLEGSE-DRIITITGTQD 61
Query: 462 AVQEALFQITTRLRHH---FF 479
+Q A + + ++ + FF
Sbjct: 62 QIQNAQYLLQNSVKQYSGKFF 82
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 340 RSLKQETGCDIKVMEAVSGTEDRLIVISG 368
+ ++ E+G IK+ E + G+EDR+I I+G
Sbjct: 30 KQIRHESGASIKIDEPLEGSEDRIITITG 58
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 20/77 (25%)
Query: 193 VLSTQV-------GCLLGKGGCVIKQIDKLPTCALASDE--------VVQITGEVDTVRK 237
+++TQV G ++GKGG IKQI ++ DE ++ ITG D ++
Sbjct: 6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQN 65
Query: 238 ALKLISHQLLDNSPRDH 254
A LL NS + +
Sbjct: 66 A-----QYLLQNSVKQY 77
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 37/154 (24%), Positives = 76/154 (49%), Gaps = 28/154 (18%)
Query: 342 LKQETGCDIKVMEA---VSGTEDRLIVISGPAHPDDRISA---------PQD-------A 382
L++ETG IK+ ++ GT +R+ +I G + + PQ+ +
Sbjct: 31 LQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNVAKTEPVS 90
Query: 383 VLRVQTRIARAIPDNREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQ 442
+L+ QT + PD Q +++V ++ G ++GKGG+ + + + SGA++++ Q
Sbjct: 91 ILQPQTTVN---PDRANQV---KIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQL---SQ 141
Query: 443 IPKCASENEEVVLINGEFEAVQEALFQITTRLRH 476
P + VV ++GE E ++A+ I +++
Sbjct: 142 KPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 48/217 (22%), Positives = 92/217 (42%), Gaps = 61/217 (28%)
Query: 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET---VSGSDERLVVIEASDNKKE 103
+VL P +IGK G+ + Q+ ++TG TI++ ++ G+ ER+ +I+
Sbjct: 7 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG------ 60
Query: 104 TSENLEASIERSENNGREEASVADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALLLV 163
T E L A + G +EK Q +
Sbjct: 61 TIEALNA---------------------------------VHGFIAEKIREMPQN--VAK 85
Query: 164 FERMVEVEPETEVA-DQENTKSSKFVLRLLVLSTQVGCLLGKGGCVIK----------QI 212
E + ++P+T V D+ N ++++V ++ G ++GKGG +K Q+
Sbjct: 86 TEPVSILQPQTTVNPDRANQ------VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQL 139
Query: 213 DKLPTCALASDEVVQITGEVDTVRKALKLISHQLLDN 249
+ P + VV ++GE + RKA++LI ++ ++
Sbjct: 140 SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 405 RLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRI-LGKDQIPKCASENEEVVLINGEFEAV 463
++L+ S G ++GKGG I +++K +GA I++ KD P E V LI G EA+
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP---GTTERVCLIQGTIEAL 65
Query: 464 QEALFQITTRLRH 476
I ++R
Sbjct: 66 NAVHGFIAEKIRE 78
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 38.5 bits (88), Expect = 0.012, Method: Composition-based stats.
Identities = 37/153 (24%), Positives = 76/153 (49%), Gaps = 28/153 (18%)
Query: 342 LKQETGCDIKVMEA---VSGTEDRLIVISGPAHPDDRI---------SAPQD-------A 382
L++ETG IK+ ++ GT +R+ +I G + + PQ+ +
Sbjct: 31 LQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREXPQNVAKTEPVS 90
Query: 383 VLRVQTRIARAIPDNREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQ 442
+L+ QT + PD Q +++V ++ G ++GKGG+ + + + SGA++++ Q
Sbjct: 91 ILQPQTTVN---PDRANQV---KIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQL---SQ 141
Query: 443 IPKCASENEEVVLINGEFEAVQEALFQITTRLR 475
P + VV ++GE E ++A+ I +++
Sbjct: 142 KPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQ 174
Score = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 48/216 (22%), Positives = 92/216 (42%), Gaps = 61/216 (28%)
Query: 48 FRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET---VSGSDERLVVIEASDNKKET 104
+VL P +IGK G+ + Q+ ++TG TI++ ++ G+ ER+ +I+ T
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG------T 61
Query: 105 SENLEASIERSENNGREEASVADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALLLVF 164
E L A + G +EK Q +
Sbjct: 62 IEALNA---------------------------------VHGFIAEKIREXPQN--VAKT 86
Query: 165 ERMVEVEPETEV-ADQENTKSSKFVLRLLVLSTQVGCLLGKGGCVIK----------QID 213
E + ++P+T V D+ N ++++V ++ G ++GKGG +K Q+
Sbjct: 87 EPVSILQPQTTVNPDRANQ------VKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLS 140
Query: 214 KLPTCALASDEVVQITGEVDTVRKALKLISHQLLDN 249
+ P + VV ++GE + RKA++LI ++ ++
Sbjct: 141 QKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176
Score = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 405 RLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRI-LGKDQIPKCASENEEVVLINGEFEAV 463
++L+ S G ++GKGG I +++K +GA I++ KD P E V LI G EA+
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP---GTTERVCLIQGTIEAL 65
Query: 464 QEALFQITTRLR 475
I ++R
Sbjct: 66 NAVHGFIAEKIR 77
Score = 28.9 bits (63), Expect = 9.4, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPK---PGATETVIIISGTPEQTHAAQSLI 652
I G+ G + Q+++ + A I ++ K PG TE V +I GT E +A I
Sbjct: 20 IIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFI 72
>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 = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 403 MTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQ-IPKCASENEEVVLINGEFE 461
+ + V N +G +LGKGG + E ++L+GA I+I K + +P + N V I G
Sbjct: 4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP--GTRNRRVT-ITGSPA 60
Query: 462 AVQEALFQITTRLRH 476
A Q A + I+ R+ +
Sbjct: 61 ATQAAQYLISQRVTY 75
Score = 32.7 bits (73), Expect = 0.59, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPK---PGATETVIIISGTPEQTHAAQSLIQAFVMSE 659
I G+ G L + ++++ A+I I+ PG + I+G+P T AAQ LI V E
Sbjct: 17 ILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYE 76
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 37.7 bits (86), Expect = 0.023, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 403 MTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQ-IPKCASENEEVVLINGEFE 461
+ + V N +G +LGKGG + E ++L+G I+I K + +P + N +V I G
Sbjct: 4 VVEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLP--GTRNRKVT-ITGTPA 60
Query: 462 AVQEALFQITTRL 474
A Q A + IT R+
Sbjct: 61 ATQAAQYLITQRI 73
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPK---PGATETVIIISGTPEQTHAAQSLI 652
I G+ G L + ++++ +I I+ PG + I+GTP T AAQ LI
Sbjct: 17 ILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAAQYLI 69
>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 = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 403 MTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQ-IPKCASENEEVVLINGEFE 461
+ + V N +G +LGKGG + E ++L+GA I+I K + +P + N V I G
Sbjct: 4 LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP--GTRNRRVT-ITGSPA 60
Query: 462 AVQEALFQITTRLRH 476
A Q A + I+ R+ +
Sbjct: 61 ATQAAQYLISQRVTY 75
Score = 32.3 bits (72), Expect = 0.79, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 603 IQGEDGACLKQIRQISDAKITITDPK---PGATETVIIISGTPEQTHAAQSLIQAFVMSE 659
I G+ G L + ++++ A+I I+ PG + I+G+P T AAQ LI V E
Sbjct: 17 ILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYE 76
>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 = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%)
Query: 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETSE 106
M V P + VIG++GEM+ +I D GV I+ + + ER+ I ++ + +
Sbjct: 4 MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAA 63
Query: 107 NLEASIERS 115
+ + RS
Sbjct: 64 EIITDLLRS 72
Score = 32.3 bits (72), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 43 PGGIM-FRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVE 82
PGG+ F + P K +IGK GE + ISQ +G I ++
Sbjct: 100 PGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQ 140
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 32.7 bits (73), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEE 83
+ V PV KI VIG +M++QI +DTG I +E+
Sbjct: 599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED 635
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 6/47 (12%)
Query: 56 KIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKK 102
KI VIGK G ++ ++++TG TI +E D+ V I A+D +K
Sbjct: 570 KIKDVIGKGGSVIRALTEETGTTIEIE------DDGTVKIAATDGEK 610
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 27/55 (49%)
Query: 602 IIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFV 656
I G G + +I+Q S KI I G E +++GTPE +A+ L+ V
Sbjct: 28 FIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIV 82
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEE 83
+ V PV KI VIG + ++QI +DTG I +E+
Sbjct: 599 IITVKIPVDKIGEVIGPKRQXINQIQEDTGAEITIED 635
>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 = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 401 TVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEF 460
T+ RLL ++G ++GK G + + R+ SGA I I + P E ++ + G
Sbjct: 4 TLTIRLLXHGKEVGSIIGKKGESVKKXREESGARINI-SEGNCP------ERIITLAGPT 56
Query: 461 EAVQEALFQITTRL 474
A+ +A I +L
Sbjct: 57 NAIFKAFAXIIDKL 70
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 23 KEKSQKLAGDYSENQPSKSFPGGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVE 82
+E+ Q GD N+ GGI V P + VIG+ GEM+ +I D GV I+ +
Sbjct: 72 RERDQGGFGD--RNEYGSRIGGGI--DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFK 127
Query: 83 E 83
+
Sbjct: 128 Q 128
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
0.315 0.133 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,287,192
Number of Sequences: 62578
Number of extensions: 779491
Number of successful extensions: 1141
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1052
Number of HSP's gapped (non-prelim): 109
length of query: 663
length of database: 14,973,337
effective HSP length: 105
effective length of query: 558
effective length of database: 8,402,647
effective search space: 4688677026
effective search space used: 4688677026
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)