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= 023320
(284 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 44/95 (46%), Gaps = 11/95 (11%)
Query: 37 TLFVSGLPDDVRAREIHNLF-----RRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVAA 91
L++ L V R++ +LF ++ P F + RG AF TF N + A A
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQ---AFITFPNKEIAWQA 83
Query: 92 LHELNGVKFDPQSGSVLHIELARSNSRKKRKPGSG 126
LH +NG K G +L IE ++ ++ P SG
Sbjct: 84 LHLVNGYKL---YGKILVIEFGKNKKQRSSGPSSG 115
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 4/89 (4%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVAALHELNG 97
++V LP D+R ++I ++F + LK RG AF F + + A A++ +G
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK-NRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 98 VKFDPQSGSVLHIELARSNSRKKRKPGSG 126
+D G L +E RS P SG
Sbjct: 84 YDYD---GYRLRVEFPRSGRGTGSGPSSG 109
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 204 LFIANLGPNCTEDELKQTLSVYPGFNMLKMR-ARGGMPVAFADFEEVEQASIAMEG 258
+++ NL P+ +++ Y + ++ RGG P AF +FE+ A A+ G
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 80
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 199 QPCSTLFIANLGPNCTEDELKQTLSVYPGFNMLKMRARGGMP-VAFADFEEVEQASIAME 257
QP TLF+ L + TE+ LK++ ++ R G F DF E A A E
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 258 GLQDSTLPSSDRGGMHIEYARSK 280
++D + D + +++A+ K
Sbjct: 73 AMEDGEI---DGNKVTLDWAKPK 92
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 200 PCSTLFIANLGPNCTEDELKQTLSVYPGFNMLKMRARGGMPVAFADFEEVEQASIAMEGL 259
P LF+ NL E L + +PGF +++ G +AF +F+ QA A + L
Sbjct: 12 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFDNEVQAGAARDAL 70
Query: 260 QDSTLPSSDRGGMHIEYAR 278
Q + + M I +A+
Sbjct: 71 QGFKI--TQNNAMKISFAK 87
Score = 31.2 bits (69), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 36 NTLFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVAALHEL 95
+ LF++ LP++ + LF + PGF +L GR + +AF F N A AA L
Sbjct: 14 HILFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHD--IAFVEFDNEVQAGAARDAL 70
Query: 96 NGVK 99
G K
Sbjct: 71 QGFK 74
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 200 PCSTLFIANLGPNCTEDELKQTLSVYPGFNMLKMRARGGMPVAFADFEEVEQASIAMEGL 259
P LF+ NL E L + +PGF +++ G +AF +F+ QA A + L
Sbjct: 206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHDIAFVEFDNEVQAGAARDAL 264
Query: 260 QDSTLPSSDRGGMHIEYAR 278
Q + + M I +A+
Sbjct: 265 QGFKI--TQNNAMKISFAK 281
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 36 NTLFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVAALHEL 95
+ LF++ LP++ + LF + PGF +L GR + +AF F N A AA L
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRL-VPGRHD--IAFVEFDNEVQAGAARDAL 264
Query: 96 NGVKF 100
G K
Sbjct: 265 QGFKI 269
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 27/104 (25%), Positives = 52/104 (50%), Gaps = 9/104 (8%)
Query: 32 DNGINTLFVSGLPDDVRAREIHNLFRRKPGFDFCQLKY---TGRGNQVVAFATFVNHQTA 88
D + ++FV +P + ++ ++F +L Y TG+ + F + + +TA
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGK-PKGYGFCEYQDQETA 63
Query: 89 VAALHELNGVKFDPQSGSVLHIELARSNSRKK--RKPGSGAYVV 130
++A+ LNG +F SG L ++ A S K+ + G+GA V+
Sbjct: 64 LSAMRNLNGREF---SGRALRVDNAASEKNKEELKSLGTGAPVI 104
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 46/95 (48%), Gaps = 10/95 (10%)
Query: 33 NGINTLFVSGLPDDVRAREIHNLFRRKPGFDFCQL-KYTGRGNQVVAFATFVNHQTAVAA 91
+G + + + GLP DV +E+H+L +C + KY G AF T +N + A AA
Sbjct: 3 SGSSGILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKG-----TAFVTLLNGEQAEAA 56
Query: 92 LHELNGVKFDPQSGSVLHIELARSNSRKKRKPGSG 126
++ + + + L ++L +++ P SG
Sbjct: 57 INTFHQSRLRERE---LSVQLQPTDALLCSGPSSG 88
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQ-LKYTGRGNQVVAFATFVNHQTAVAALHELN 96
LFV L ++ LF+ D C L+ ++ AF F +H A AA+H L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 97 GVKFDPQSGSVLHIELARSNSRKKRKPGSG 126
G + P + S L ++ A ++ K+ P SG
Sbjct: 78 GSQTMPGASSSLVVKFA--DTDKESGPSSG 105
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 16/83 (19%)
Query: 189 NSEKPYEGGVQPCSTLFIANLGPNCTEDELKQTLSVY-----------PGFNMLKMRARG 237
N KP E S LF+ NL P+ TE+E+++ Y GF +++ R
Sbjct: 10 NFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETR- 68
Query: 238 GMPVAFADFEEVEQASIAMEGLQ 260
A+ +VE ++ + G Q
Sbjct: 69 ----TLAEIAKVELDNMPLRGKQ 87
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 8/94 (8%)
Query: 33 NGINTLFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVAAL 92
+G + + V LP D +E+H+L + +C Y R N+ AF T +N + A A+
Sbjct: 3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYC---YVDR-NKRTAFVTLLNGEQAQNAI 57
Query: 93 HELNGVKFDPQSGSVLHIELARSNSRKKRKPGSG 126
+ F G L ++L +++ P SG
Sbjct: 58 QMFHQYSF---RGKDLIVQLQPTDALLCSGPSSG 88
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 38/90 (42%), Gaps = 3/90 (3%)
Query: 37 TLFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVAALHELN 96
TL+V L DV I LF + C++ N F F H+ A AAL +N
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 97 GVKFDPQSGSVLHIELARSNSRKKRKPGSG 126
G K G + + A + S +K P SG
Sbjct: 77 GRKI---LGKEVKVNWATTPSSQKSGPSSG 103
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 31.2 bits (69), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQLK--YTGRGNQVVAFATFVNHQTAVAALHEL 95
L V+ LP D+ RE++ LFR + C++ Y + AF F + + A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGV 98
NG+
Sbjct: 66 NGI 68
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 31.2 bits (69), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 202 STLFIANLGPNCTEDELKQTLSVY-PGFNMLKMRARGGMPVAFADFEEVEQASIAMEGLQ 260
+ L + N+ P CT EL+ Y P ++ AF E E A A+ GL
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-----DYAFVHMERAEDAVEAIRGL- 64
Query: 261 DSTLPSSDRGGMHIEYARSKMR 282
D+T R MH++ + S++R
Sbjct: 65 DNTEFQGKR--MHVQLSTSRLR 84
>pdb|3H2V|E Chain E, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|F Chain F, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|G Chain G, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|H Chain H, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
Length = 74
Score = 30.8 bits (68), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 35 INTLFVSGLPDDVRAREIHNLFRRKPGFDFCQL-KYTGRGNQVVAFATFVNHQTAVAALH 93
+ + + GLP DV +E+H+L +C + KY G AF T +N + A AA++
Sbjct: 2 MRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKG-----TAFVTLLNGEQAEAAIN 55
Query: 94 ELNGVKFDPQSGSV 107
+ + + SV
Sbjct: 56 AFHQSRLRERELSV 69
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 50/99 (50%), Gaps = 20/99 (20%)
Query: 198 VQPCSTLFIANLGPNCTEDELKQTL-SVYPGFN-------MLKMRARGGMPVAFADFEEV 249
++P T++I N+ ++ELK++L +++ F + M+ RG AF F+E+
Sbjct: 3 IRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQ---AFVIFKEL 59
Query: 250 EQASIAMEGLQDSTLPSSDRGGMHIEYAR------SKMR 282
++ A+ LQ P + M I+YA+ SKMR
Sbjct: 60 GSSTNALRQLQG--FPFYGK-PMRIQYAKTDSDIISKMR 95
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 30.8 bits (68), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQL-KYTGRGNQVVAFATFVNHQTAVAALHELN 96
+ + GLP DV +E+H+L +C + KY G AF T +N + A AA++ +
Sbjct: 23 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKG-----TAFVTLLNGEQAEAAINAFH 76
Query: 97 GVKFDPQSGSV 107
+ + SV
Sbjct: 77 QSRLRERELSV 87
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 204 LFIANLGPNCTEDELKQTLSVYPGFNMLKMRA-RGGMP--VAFADFEEVEQASIAMEGLQ 260
LFI+ L +CT++EL++ + L++ R G P +A+ ++E QAS A+ +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 261 DSTL 264
T+
Sbjct: 80 GMTI 83
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQL-KYTGRGNQVVAFATFVNHQTAVAALHELN 96
+ + GLP DV +E+H+L +C + KY G AF T +N + A AA++ +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKG-----TAFVTLLNGEQAEAAINAFH 78
Query: 97 GVKFDPQSGSV 107
+ + SV
Sbjct: 79 QSRLRERELSV 89
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQL-KYTGRGNQVVAFATFVNHQTAVAALHELN 96
+ + GLP DV +E+H+L +C + KY G AF T +N + A AA++ +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKG-----TAFVTLLNGEQAEAAINAFH 78
Query: 97 GVKFDPQSGSV 107
+ + SV
Sbjct: 79 QSRLRERELSV 89
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 197 GVQPCSTLFIANLGPNCTEDELKQTLS---VYPGFNMLKMRARGG----MPVAFADFEEV 249
G S LFI NL + TE+ LK S + K + + G M F ++++
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 250 EQASIAMEGLQDSTL 264
EQA A++ LQ T+
Sbjct: 61 EQAQKALKQLQGHTV 75
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 16/70 (22%)
Query: 202 STLFIANLGPNCTEDELKQTLSVY-----------PGFNMLKMRARGGMPVAFADFEEVE 250
S LF+ NL P+ TE+E+++ Y GF +++ R A+ +VE
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETR-----TLAEIAKVE 70
Query: 251 QASIAMEGLQ 260
++ + G Q
Sbjct: 71 LDNMPLRGKQ 80
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
Length = 184
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQLK--YTGRGNQVVAFATFVNHQTAVAALHEL 95
L V+ LP D RE++ LFR + C++ Y + AF F + + A+ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 96 NGV 98
NG+
Sbjct: 77 NGI 79
>pdb|1ZYQ|A Chain A, T7 Dna Polymerase In Complex With 8og And Incoming Ddatp
Length = 698
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 60 PGFDFCQLKYTGRGNQVVAFATFVNHQTA-VAALHELNGVKFDPQSGSVLHIELARSNSR 118
P DF + YT ++ + A + H+ A + A E NG FD ++ L++ELA S
Sbjct: 188 PEIDFTDVGYTTFWSESLE-AVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSE 246
Query: 119 KKRK 122
RK
Sbjct: 247 LLRK 250
>pdb|1T7P|A Chain A, T7 Dna Polymerase Complexed To Dna PrimerTEMPLATE,A
Nucleoside Triphosphate, And Its Processivity Factor
Thioredoxin
pdb|1SKR|A Chain A, T7 Dna Polymerase Complexed To Dna Primer/template And
Ddatp
pdb|1SKS|A Chain A, Binary 3' Complex Of T7 Dna Polymerase With A Dna
PrimerTEMPLATE CONTAINING A CIS-Syn Thymine Dimer On The
Template
pdb|1SKW|A Chain A, Binary 3' Complex Of T7 Dna Polymerase With A Dna
PrimerTEMPLATE CONTAINING A DISORDERED CIS-Syn Thymine
Dimer On The Template
pdb|1SL0|A Chain A, Ternary 3' Complex Of T7 Dna Polymerase With A Dna
PrimerTEMPLATE CONTAINING A DISORDERED CIS-Syn Thymine
Dimer On The Template And An Incoming Nucleotide
pdb|1SL0|C Chain C, Ternary 3' Complex Of T7 Dna Polymerase With A Dna
PrimerTEMPLATE CONTAINING A DISORDERED CIS-Syn Thymine
Dimer On The Template And An Incoming Nucleotide
pdb|1SL1|A Chain A, Binary 5' Complex Of T7 Dna Polymerase With A Dna
Primer/template Containing A Cis-syn Thymine Dimer On
The Template
pdb|1SL2|A Chain A, Ternary 5' Complex Of T7 Dna Polymerase With A Dna
PrimerTEMPLATE CONTAINING A CIS-Syn Thymine Dimer On The
Template And An Incoming Nucleotide
pdb|1TK0|A Chain A, T7 Dna Polymerase Ternary Complex With 8 Oxo Guanosine And
Ddctp At The Insertion Site
pdb|1TK5|A Chain A, T7 Dna Polymerase Binary Complex With 8 Oxo Guanosine In
The Templating Strand
pdb|1TK8|A Chain A, T7 Dna Polymerase Ternary Complex With 8 Oxo Guanosine And
Damp At The Elongation Site
pdb|1TKD|A Chain A, T7 Dna Polymerase Ternary Complex With 8 Oxo Guanosine And
Dcmp At The Elongation Site
pdb|1T8E|A Chain A, T7 Dna Polymerase Ternary Complex With Dctp At The
Insertion Site.
pdb|1X9M|A Chain A, T7 Dna Polymerase In Complex With An N-2-
Acetylaminofluorene-adducted Dna
pdb|1X9S|A Chain A, T7 Dna Polymerase In Complex With A PrimerTEMPLATE DNA
Containing A Disordered N-2 Aminofluorene On The
Template, Crystallized With Dideoxy-Ctp As The Incoming
Nucleotide.
pdb|1X9W|A Chain A, T7 Dna Polymerase In Complex With A Primer/template Dna
Containing A Disordered N-2 Aminofluorene On The
Template, Crystallized With Dideoxy-atp As The Incoming
Nucleotide
Length = 698
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 60 PGFDFCQLKYTGRGNQVVAFATFVNHQTA-VAALHELNGVKFDPQSGSVLHIELARSNSR 118
P DF + YT ++ + A + H+ A + A E NG FD ++ L++ELA S
Sbjct: 188 PEIDFTDVGYTTFWSESLE-AVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSE 246
Query: 119 KKRK 122
RK
Sbjct: 247 LLRK 250
>pdb|2AJQ|A Chain A, Structure Of Replicative Dna Polymerase Provides Insigts
Into The Mechanisms For Processivity, Frameshifting And
Editing
pdb|2AJQ|F Chain F, Structure Of Replicative Dna Polymerase Provides Insigts
Into The Mechanisms For Processivity, Frameshifting And
Editing
Length = 704
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 60 PGFDFCQLKYTGRGNQVVAFATFVNHQTA-VAALHELNGVKFDPQSGSVLHIELARSNSR 118
P DF + YT ++ + A + H+ A + A E NG FD ++ L++ELA S
Sbjct: 194 PEIDFTDVGYTTFWSESLE-AVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSE 252
Query: 119 KKRK 122
RK
Sbjct: 253 LLRK 256
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/97 (19%), Positives = 44/97 (45%), Gaps = 5/97 (5%)
Query: 31 QDNGINTLFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVA 90
+ +G+ +F+ L + + +++ F C++ G++ F F + A
Sbjct: 94 RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAER 153
Query: 91 ALHELNGVKFDPQSGSVLHIELARSNSRKKRKPGSGA 127
A+ ++NG+ + + + + R SRK+R+ GA
Sbjct: 154 AIEKMNGMLLNDRK-----VFVGRFKSRKEREAELGA 185
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/97 (19%), Positives = 44/97 (45%), Gaps = 5/97 (5%)
Query: 31 QDNGINTLFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVA 90
+ +G+ +F+ L + + +++ F C++ G++ F F + A
Sbjct: 99 RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAER 158
Query: 91 ALHELNGVKFDPQSGSVLHIELARSNSRKKRKPGSGA 127
A+ ++NG+ + + + + R SRK+R+ GA
Sbjct: 159 AIEKMNGMLLNDR-----KVFVGRFKSRKEREAELGA 190
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 29.3 bits (64), Expect = 2.5, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQL--KYTGRGNQVVAFATFVNHQTAVAALHEL 95
L V+ LP D+ RE++ LFR + C++ Y + AF F + + A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGV 98
NG+
Sbjct: 66 NGI 68
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 29.3 bits (64), Expect = 2.8, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 200 PCSTLFIANLGPNCTEDELKQTLSVYPGFNMLKMRARGGMPVAFADFEEVEQASIAMEGL 259
P LF+ NL E L + +PGF +++ +AF +F Q++ A E L
Sbjct: 7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRL-VPNRHDIAFVEFTTELQSNAAKEAL 65
Query: 260 Q 260
Q
Sbjct: 66 Q 66
Score = 28.9 bits (63), Expect = 3.0, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 38 LFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVAALHELNG 97
LF++ LP++ + LF + PGF +L +AF F + AA L G
Sbjct: 11 LFLTNLPEETNEMMLSMLFNQFPGFKEVRLV---PNRHDIAFVEFTTELQSNAAKEALQG 67
Query: 98 VKFDP 102
K P
Sbjct: 68 FKITP 72
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 204 LFIANLGPNCTEDELKQTLSVYPGFN---MLKMRARGGMPVAFADFEEVEQASIAME 257
LFI NL PN + ELK +S N ++ +R + DFE E A+E
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE 72
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 191 EKPYEGGVQPCS-TLFIANLGPNCTEDELKQTLSVYPGFN---MLKMRARGGMPVAFADF 246
E P EG LFI NL PN + ELK +S N ++ +R + DF
Sbjct: 6 EDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 65
Query: 247 EEVEQASIAME 257
E E A+E
Sbjct: 66 ESAEDLEKALE 76
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 27.7 bits (60), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 17/90 (18%), Positives = 40/90 (44%), Gaps = 5/90 (5%)
Query: 34 GINTLFVSGLPDDVRAREIHNLFRRKPGFDFCQLKYTGRGNQVVAFATFVNHQTAVAALH 93
G+ +F+ L + + +++ F C++ G++ F F + A A+
Sbjct: 10 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 69
Query: 94 ELNGVKFDPQSGSVLHIELARSNSRKKRKP 123
++NG+ + + + + R SRK+R+
Sbjct: 70 KMNGMLLNDRK-----VFVGRFKSRKEREA 94
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 37 TLFVSGLPDDVRAREIHNLFRRKPGFDFCQL---KYTGRGNQVVAFATFVNHQTAVAALH 93
T+ V+ L +D R ++ LFR L K TG+ ++ AF +F + A A+
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQ-SKGFAFISFHRREDAARAIA 75
Query: 94 ELNGVKFDPQSGSVLHIELAR 114
++G +D +L++E A+
Sbjct: 76 GVSGFGYDHL---ILNVEWAK 93
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
0.314 0.130 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,506,158
Number of Sequences: 62578
Number of extensions: 302657
Number of successful extensions: 504
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 489
Number of HSP's gapped (non-prelim): 43
length of query: 284
length of database: 14,973,337
effective HSP length: 98
effective length of query: 186
effective length of database: 8,840,693
effective search space: 1644368898
effective search space used: 1644368898
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)