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= 010373
(512 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 = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 46/157 (29%), Positives = 75/157 (47%), Gaps = 33/157 (21%)
Query: 68 QLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAE 127
++R E+ + I ISE C ERI+T+ + +A+F+ I+
Sbjct: 29 KMREESGARINISEG--NCPERIITLAGPT-----------------NAIFKAFAMII-- 67
Query: 128 DSLADDEFGELT--------LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
D L +D +T +T+R++VPA Q G +IGKGG I+ IR T AQ+++ D
Sbjct: 68 DKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD 127
Query: 180 EHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216
LP S + + +AG P + + + QI + E
Sbjct: 128 -MLP---NSTERAITIAGIPQSIIECVKQICVVMLET 160
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 28/38 (73%)
Query: 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRI 382
P +T R++VP++Q G LIG+GG I E+R +T A +++
Sbjct: 87 PPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQV 124
Score = 37.0 bits (84), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 7/76 (9%)
Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
+T+R+L+ ++G +IGK G+ ++ +R E+ A+I I + + P + ++ +AG
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAGPTN 57
Query: 201 VVRKALVQIASRLHEN 216
+ KA I +L E+
Sbjct: 58 AIFKAFAMIIDKLEED 73
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 76/160 (47%), Gaps = 22/160 (13%)
Query: 68 QLRSETKSNIRISET---VPGCDERIVTIYSSSEGTNLFEDSGEFVS------PAQDALF 118
QL+ ET + I++S++ PG ER+ I + E N F++ P A
Sbjct: 30 QLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHG---FIAEKIREXPQNVAKT 86
Query: 119 RVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI-L 177
+ + ++ D + V+++VP G +IGKGG ++ I ++ A +++
Sbjct: 87 EPVSILQPQTTVNPDRANQ-----VKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQ 141
Query: 178 KDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP 217
K + + L + ++ V+GEP RKA+ I ++ E+P
Sbjct: 142 KPDGINLQ----NRVVTVSGEPEQNRKAVELIIQKIQEDP 177
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL 182
+++L+P+ G +IGKGGQ I ++ ET A I++ K +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF 47
Score = 32.3 bits (72), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 23/33 (69%)
Query: 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRI 382
++L+PS G +IG+GG I +++ T A+I++
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKL 41
Score = 32.0 bits (71), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 31/136 (22%), Positives = 57/136 (41%), Gaps = 15/136 (11%)
Query: 261 EFSLRLVCPAXXXXXXXXXXXXXXXXXRQESGASIKVDSS-----GAEGDDCIIFISTKE 315
++ L+++ P+ ++E+GA+IK+ S G C+I T E
Sbjct: 5 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQ-GTIE 63
Query: 316 FFEDPSPTITAALRLQPRCSEKTERES---------GDPVITTRILVPSAQIGCLIGRGG 366
I +R P+ KTE S D +I+VP++ G +IG+GG
Sbjct: 64 ALNAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGG 123
Query: 367 AIISEMRSATRASIRI 382
A + + + A +++
Sbjct: 124 ATVKAIXEQSGAWVQL 139
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 76/160 (47%), Gaps = 22/160 (13%)
Query: 68 QLRSETKSNIRISET---VPGCDERIVTIYSSSEGTNLFEDSGEFVS------PAQDALF 118
QL+ ET + I++S++ PG ER+ I + E N F++ P A
Sbjct: 30 QLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHG---FIAEKIREMPQNVAKT 86
Query: 119 RVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI-L 177
+ + ++ D + V+++VP G +IGKGG ++ I ++ A +++
Sbjct: 87 EPVSILQPQTTVNPDRANQ-----VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQ 141
Query: 178 KDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP 217
K + + L + ++ V+GEP RKA+ I ++ E+P
Sbjct: 142 KPDGINLQ----NRVVTVSGEPEQNRKAVELIIQKIQEDP 177
Score = 34.3 bits (77), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL 182
+++L+P+ G +IGKGGQ I ++ ET A I++ K +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF 47
Score = 32.3 bits (72), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 30/141 (21%), Positives = 64/141 (45%), Gaps = 25/141 (17%)
Query: 261 EFSLRLVCPAXXXXXXXXXXXXXXXXXRQESGASIKVDSS-----GAEGDDCII------ 309
++ L+++ P+ ++E+GA+IK+ S G C+I
Sbjct: 5 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA 64
Query: 310 ------FISTK--EFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCL 361
FI+ K E ++ + T ++ LQP+ + +R + +I+VP++ G +
Sbjct: 65 LNAVHGFIAEKIREMPQNVAKTEPVSI-LQPQTTVNPDRAN-----QVKIIVPNSTAGLI 118
Query: 362 IGRGGAIISEMRSATRASIRI 382
IG+GGA + + + A +++
Sbjct: 119 IGKGGATVKAIMEQSGAWVQL 139
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 7/84 (8%)
Query: 343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQIT 402
G P+ITT++ +P G +IG+GG I ++R + ASI+I + P ED ++ IT
Sbjct: 10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSED-RIITIT 64
Query: 403 GSLDVASSA--LSQVTLRLRANTF 424
G+ D +A L Q +++ + F
Sbjct: 65 GTQDQIQNAQYLLQNSVKQYSGKF 88
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 7/73 (9%)
Query: 135 FGELT--LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDEL 192
+G+L +IT ++ +P D G +IGKGGQ I+ IR E+ A I+I DE PL S D +
Sbjct: 6 YGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DE--PLEG-SEDRI 60
Query: 193 LQVAGEPAVVRKA 205
+ + G ++ A
Sbjct: 61 ITITGTQDQIQNA 73
>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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 5/67 (7%)
Query: 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS 404
P+ITT++ +P G +IG+GG I ++R + ASI+I + P ED ++ ITG+
Sbjct: 5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSED-RIITITGT 59
Query: 405 LDVASSA 411
D +A
Sbjct: 60 QDQIQNA 66
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199
+IT ++ +P D G +IGKGGQ I+ IR E+ A I+I DE PL S D ++ + G
Sbjct: 6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DE--PLEG-SEDRIITITGTQ 60
Query: 200 AVVRKA 205
++ A
Sbjct: 61 DQIQNA 66
>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 = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 7/77 (9%)
Query: 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199
++T+R+L+ ++G +IGK G+ ++ IR E+ A+I I + S + ++ + G
Sbjct: 2 MLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN-------SPERIITLTGPT 54
Query: 200 AVVRKALVQIASRLHEN 216
+ KA I +L E+
Sbjct: 55 NAIFKAFAMIIDKLEED 71
Score = 29.3 bits (64), Expect = 4.8, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL 405
++T R+L+ ++G +IG+ G + +R + A I I + N P E ++ +TG
Sbjct: 2 MLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI-SEGNSP------ERIITLTGPT 54
Query: 406 DVASSALSQVTLRLRAN 422
+ A + + +L +
Sbjct: 55 NAIFKAFAMIIDKLEED 71
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 7/84 (8%)
Query: 343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQIT 402
G P+ITT++ +P +IG+GG I ++R + ASI+I + P ED ++ IT
Sbjct: 10 GGPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI----DEPLEGSED-RIITIT 64
Query: 403 GSLDVASSA--LSQVTLRLRANTF 424
G+ D +A L Q +++ + F
Sbjct: 65 GTQDQIQNAQYLLQNSVKQYSGKF 88
Score = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 133 DEFGEL--TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFD 190
+ +G+L +IT ++ +P D +IGKGGQ I+ IR E+ A I+I DE PL S D
Sbjct: 4 NSYGDLGGPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI--DE--PLEG-SED 58
Query: 191 ELLQVAGEPAVVRKA 205
++ + G ++ A
Sbjct: 59 RIITITGTQDQIQNA 73
>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 = 38.1 bits (87), Expect = 0.012, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199
++T+R+L+ ++G +IGK G+ ++ IR E+ A+I I + + P + ++ + G
Sbjct: 2 ILTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI-SEGNCP------ERIITLTGPT 54
Query: 200 AVVRKALVQIASRLHEN 216
+ KA I +L E+
Sbjct: 55 NAIFKAFAMIIDKLEED 71
Score = 30.0 bits (66), Expect = 3.1, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL 405
++T R+L+ ++G +IG+ G + +R + A I I + N P E ++ +TG
Sbjct: 2 ILTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI-SEGNCP------ERIITLTGPT 54
Query: 406 DVASSALSQVTLRLRAN 422
+ A + + +L +
Sbjct: 55 NAIFKAFAMIIDKLEED 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 = 37.4 bits (85), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASS 410
+ +P+ IGC+IGR GA I+E+R + A I+I V + V ITGS AS
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKI-----ANPVEGSTDRQVTITGS--AASI 61
Query: 411 ALSQVTLRLR 420
+L+Q + +R
Sbjct: 62 SLAQYLINVR 71
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176
+ +P D IGC+IG+ G I IR + AQI+I
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKI 40
>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 = 36.2 bits (82), Expect = 0.040, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
+T+R+L ++G +IGK G+ ++ R E+ A+I I + + P + ++ +AG
Sbjct: 5 LTIRLLXHGKEVGSIIGKKGESVKKXREESGARINI-SEGNCP------ERIITLAGPTN 57
Query: 201 VVRKALVQIASRLHEN 216
+ KA I +L E+
Sbjct: 58 AIFKAFAXIIDKLEED 73
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 36.2 bits (82), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
T + +P+ IGC+IGR GA I+E+R + A I+I V V ITGS
Sbjct: 7 THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN-----PVEGSSGRQVTITGS--A 59
Query: 408 ASSALSQVTLRLR 420
AS +L+Q + R
Sbjct: 60 ASISLAQYLINAR 72
Score = 32.3 bits (72), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176
T + +P + IGC+IG+ G I IR + AQI+I
Sbjct: 7 THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI 41
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 35.0 bits (79), Expect = 0.099, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 3/71 (4%)
Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRK 204
+++PA + G VIGKGG+ I+ ++ ++ +++D + D+ L++ G+P V++
Sbjct: 18 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ---NTNVDKPLRIIGDPYKVQQ 74
Query: 205 ALVQIASRLHE 215
A + L E
Sbjct: 75 ACEMVMDILRE 85
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 3/71 (4%)
Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRK 204
+++PA + G VIGKGG+ I+ ++ ++ +++D + D+ L++ G+P V++
Sbjct: 6 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ---NTNVDKPLRIIGDPYKVQQ 62
Query: 205 ALVQIASRLHE 215
A + L E
Sbjct: 63 ACEMVMDILRE 73
>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 = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD-EHLPLCALSFDELLQVAGEPAV 201
V M VP + +G ++GKGG+ + + T A+I+I K E LP + + + + G PA
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSPAA 61
Query: 202 VRKALVQIASRL 213
+ A I+ R+
Sbjct: 62 TQAAQYLISQRV 73
>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 = 0.25, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 37/61 (60%), Gaps = 3/61 (4%)
Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRK 204
+++PA + G VIGKGG+ I+ ++ ++ +++D A D+ L++ G+P V++
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA---DKPLRITGDPYKVQQ 75
Query: 205 A 205
A
Sbjct: 76 A 76
Score = 29.6 bits (65), Expect = 4.4, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 35/53 (66%), Gaps = 3/53 (5%)
Query: 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG 403
I++P+++ G +IG+GG I +++ RA ++++ ++ P+ D+ + +ITG
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQE--RAGVKMVMIQDGPQNTGADKPL-RITG 68
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 32.3 bits (72), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
+ITV+ +P D+IG VIG Q+I I+ +T A+I I D
Sbjct: 599 IITVK--IPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD 636
>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 = 32.0 bits (71), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD-EHLPLCALSFDELLQVAGEPAV 201
V + VP + +G ++GKGG+ + + T A+I+I K E LP + + + + G PA
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSPAA 61
Query: 202 VRKALVQIASRL 213
+ A I+ R+
Sbjct: 62 TQAAQYLISQRV 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 = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVV 202
V++ +PA +G +IGK GQ I+ + A I+I P S ++ + G P
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAP----PETPDSKVRMVIITGPPEAQ 60
Query: 203 RKALVQIASRLHE 215
KA +I +L E
Sbjct: 61 FKAQGRIYGKLKE 73
Score = 31.6 bits (70), Expect = 1.0, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 115 DALFRVHDRIVAEDSLADDEF---GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR 171
+A F+ RI + L ++ F E + + VPA G VIGKGG+ + ++ T
Sbjct: 58 EAQFKAQGRIYGK--LKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTA 115
Query: 172 AQIRILKDE 180
A++ + +D+
Sbjct: 116 AEVVVPRDQ 124
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
+ T I VP++ G +IG+GG ++E+++ T A + ++ + P D+ +V+I G
Sbjct: 85 LETHIRVPASAAGRVIGKGGKTVNELQNLTAAEV-VVPRDQTPD--ENDQVIVKIIGHF- 140
Query: 407 VASSALSQVTLR 418
+S ++Q +R
Sbjct: 141 -YASQMAQRKIR 151
Score = 31.2 bits (69), Expect = 1.6, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVAS 409
++ +P+ +G +IG+ G I ++ ASI+I P+ MV ITG +
Sbjct: 6 QVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAP----PETPDSKVRMVIITGPPEAQF 61
Query: 410 SALSQVTLRLRANTF 424
A ++ +L+ F
Sbjct: 62 KAQGRIYGKLKEENF 76
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
+ITV+ +P D+IG VIG Q I I+ +T A+I I D
Sbjct: 599 IITVK--IPVDKIGEVIGPKRQXINQIQEDTGAEITIEDD 636
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD-EHLPLCALSFDELLQVAGEPAV 201
V + VP + +G ++GKGG+ + + T +I+I K E LP + + + + G PA
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLP---GTRNRKVTITGTPAA 61
Query: 202 VRKALVQIASRL 213
+ A I R+
Sbjct: 62 TQAAQYLITQRI 73
>pdb|1FW1|A Chain A, Glutathione Transferase ZetaMALEYLACETOACETATE ISOMERASE
Length = 216
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 44/106 (41%), Gaps = 9/106 (8%)
Query: 69 LRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAED 128
RS +RI+ + G D + V I +G F + ++P + D I
Sbjct: 12 FRSSCSWRVRIALALKGIDYKTVPINLIKDGGQQFSKDFQALNPMKQVPTLKIDGITIHQ 71
Query: 129 SLADDEFGELTLITVRMLVPAD--------QIGCVIGKGGQVIQNI 166
SLA E+ E T T R+L P D I +I G Q +QN+
Sbjct: 72 SLAIIEYLEETRPTPRLL-PQDPKKRASVRMISDLIAGGIQPLQNL 116
>pdb|2CZ2|A Chain A, Crystal Structure Of Glutathione Transferase Zeta 1-1
(Maleylacetoacetate Isomerase) From Mus Musculus (Form-1
Crystal)
pdb|2CZ3|A Chain A, Crystal Structure Of Glutathione Transferase Zeta 1-1
(Maleylacetoacetate Isomerase) From Mus Musculus (Form-2
Crystal)
pdb|2CZ3|B Chain B, Crystal Structure Of Glutathione Transferase Zeta 1-1
(Maleylacetoacetate Isomerase) From Mus Musculus (Form-2
Crystal)
Length = 223
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 44/106 (41%), Gaps = 9/106 (8%)
Query: 69 LRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAED 128
RS +RI+ + G D IV I +G F + + ++P + D I
Sbjct: 19 FRSSCSWRVRIALALKGIDYEIVPINLIKDGGQQFTEEFQTLNPXKQVPALKIDGITIVQ 78
Query: 129 SLADDEFGELTLITVRMLVPAD--------QIGCVIGKGGQVIQNI 166
SLA E+ E T R+L P D I +I G Q +QN+
Sbjct: 79 SLAIXEYLEETRPIPRLL-PQDPQKRAIVRXISDLIASGIQPLQNL 123
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 25/41 (60%)
Query: 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
+++T VP +G +IG+GG+ I I+ E+ +I+I D
Sbjct: 13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD 53
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL 405
V+T VP +G +IGRGG IS ++ + I+I P E +TG+
Sbjct: 14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI-----APDSGGLPERSCMLTGTP 68
Query: 406 DVASSA---LSQVTLRLRAN 422
+ SA L Q+ + R+
Sbjct: 69 ESVQSAKRLLDQIVEKGRSG 88
>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 = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASS 410
+ +P +G +IGR G +I ++++ A +RI + P E + QITG D A
Sbjct: 7 VPIPRFAVGIVIGRNGEMIKKIQND--AGVRI---QFKPDDGTTPERIAQITGPPDRAQH 61
Query: 411 ALSQVTLRLRA 421
A +T LR+
Sbjct: 62 AAEIITDLLRS 72
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199
+VP + G +IGKGG+ I++I ++ A+I + ++ P A +L + G P
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKLFTIRGTP 160
>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 = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 147 VPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA 186
+P D+I VIG GG+VI+ I T A++ I D + + A
Sbjct: 567 IPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSA 606
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 147 VPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA 186
+P D+I VIG GG+VI+ I T A++ I D + + A
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSA 615
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 147 VPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA 186
+P D+I VIG GG+VI+ I T A++ I D + + A
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSA 615
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE-HLPLCALSFDELLQVAG 197
T +T VP +G +IG+GG+ I I+ ++ +++I D LP ++S G
Sbjct: 14 TSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSL------TG 67
Query: 198 EPAVVRKALVQI 209
P V+KA + +
Sbjct: 68 APESVQKAKMML 79
>pdb|2E3U|A Chain A, Crystal Structure Analysis Of Dim2p From Pyrococcus
Horikoshii Ot3
pdb|3AEV|B Chain B, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 219
Score = 29.3 bits (64), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 147 VPADQIGCVIGKGGQVIQNIRTETRAQIRI 176
+P D+I +IGK GQ + I T+ +I I
Sbjct: 40 IPKDRIAVLIGKKGQTKKEIEKRTKTKITI 69
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 21/37 (56%)
Query: 150 DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA 186
D+I VIGKGG VI+ + ET I I D + + A
Sbjct: 569 DKIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKIAA 605
>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 = 28.5 bits (62), Expect = 9.4, Method: Composition-based stats.
Identities = 32/112 (28%), Positives = 50/112 (44%), Gaps = 26/112 (23%)
Query: 75 SNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDE 134
+NI+ + VPG VT E T F GE QDA+ + + E
Sbjct: 24 ANIQQARKVPG-----VTAIDLDEDTCTFHIYGE----DQDAVKKARSFL---------E 65
Query: 135 FGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTET---RAQIRILKDEHLP 183
F E + VP + +G VIGK G++IQ I ++ R +I ++++P
Sbjct: 66 FAEDVI-----QVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVP 112
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 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,879,726
Number of Sequences: 62578
Number of extensions: 460660
Number of successful extensions: 1012
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 936
Number of HSP's gapped (non-prelim): 76
length of query: 512
length of database: 14,973,337
effective HSP length: 103
effective length of query: 409
effective length of database: 8,527,803
effective search space: 3487871427
effective search space used: 3487871427
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 54 (25.4 bits)