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= 005315
(702 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 40/94 (42%), Positives = 55/94 (58%), Gaps = 10/94 (10%)
Query: 57 GFGNIIVVDNLPVVPKEKFEKLEGVI--------KEDGLWMPVDPETQKSLGYCFIEYNT 108
G ++IVVDN+P V ++ EKL+ VI K + P E K+ GY F+EY +
Sbjct: 13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYAS 70
Query: 109 PQEAELAKEKTNGYKLDRAHIFAVNMFDDFDKFM 142
P A A + +GYKLD+ H F VN+F DFDK+M
Sbjct: 71 PAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYM 104
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 10/82 (12%)
Query: 60 NIIVVDNLPVVPKEKFEKLEGVI--------KEDGLWMPVDPETQKSLGYCFIEYNTPQE 111
++IVVDN+P V ++ EKL+ VI K + P E K+ GY F+EY +P
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAH 59
Query: 112 AELAKEKTNGYKLDRAHIFAVN 133
A A + +GYKLD+ H F VN
Sbjct: 60 AVDAVKNADGYKLDKQHTFRVN 81
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 36.6 bits (83), Expect = 0.046, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 62 IVVDNLPV-VPKEKFEKLEGVIKE-DGLWMPVDPETQKSLGYCFIEYNTPQEAELAKEKT 119
++V+ LP + +E+F L G I E + + D T +SLGY F+ Y P++AE A
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 120 NGYKLDRAHI 129
NG +L I
Sbjct: 65 NGLRLQTKTI 74
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 35.8 bits (81), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 8/88 (9%)
Query: 62 IVVDNLPVVPKEKFEKLEGVI--------KEDGLWMPVDPETQKSLGYCFIEYNTPQEAE 113
IVV+ PV+P K L+ + K + P+D T K+ G+ F+E + +A+
Sbjct: 9 IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAK 68
Query: 114 LAKEKTNGYKLDRAHIFAVNMFDDFDKF 141
+ +G +LD H + D +++
Sbjct: 69 KIIKSFHGKRLDLKHRLFLYTMKDVERY 96
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 15/70 (21%)
Query: 92 DPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLDRAHIFAVNMFDDFDKFMKVPDEWAPP 151
DP T K GY FIEY Q ++ A + ++N+FD ++++V PP
Sbjct: 160 DPTTGKHKGYGFIEYEKAQSSQDA-------------VSSMNLFDLGGQYLRVGKAVTPP 206
Query: 152 EH--KPYTPG 159
P TPG
Sbjct: 207 MPLLTPATPG 216
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 35.0 bits (79), Expect = 0.15, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 22/38 (57%)
Query: 87 LWMPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
L M DP+T +S GY FIE+ + + A NGY+L
Sbjct: 33 LKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 70
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 62 IVVDNLPV-VPKEKFEKLEGVIKE-DGLWMPVDPETQKSLGYCFIEYNTPQEAELAKEKT 119
++V+ LP + +++F+ L G I + + + D T +SLGY F+ Y+ P +A+ A
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 120 NGYKLDRAHI 129
NG KL I
Sbjct: 67 NGLKLQTKTI 76
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 22/38 (57%)
Query: 87 LWMPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
L M DP+T +S GY FIE+ + + A NGY+L
Sbjct: 32 LKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 69
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 62 IVVDNLPV-VPKEKFEKLEGVIKE-DGLWMPVDPETQKSLGYCFIEYNTPQEAELAKEKT 119
++V+ LP + +++F+ L G I + + + D T +SLGY F+ Y+ P +A+ A
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 120 NGYKLDRAHI 129
NG KL I
Sbjct: 67 NGLKLQTKTI 76
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 22/38 (57%)
Query: 87 LWMPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
L M DP+T +S GY FIE+ + + A NGY+L
Sbjct: 34 LKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 71
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 34.7 bits (78), Expect = 0.20, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 57 GFGNIIVVDNLPVVPKEKFEKLEGVI--------KEDGLWMPVDPETQKSLGYCFIEYNT 108
G IVV+ PV+P K L+ + K + P+D T K+ G+ F+E +
Sbjct: 4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGS 63
Query: 109 PQEAELAKEKTNGYKLDRAH 128
+A+ + +G +LD H
Sbjct: 64 MNDAKKIIKSFHGKRLDLKH 83
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 33.5 bits (75), Expect = 0.36, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 15/70 (21%)
Query: 92 DPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLDRAHIFAVNMFDDFDKFMKVPDEWAPP 151
DP T K GY FIEY Q ++ A + + N+FD ++++V PP
Sbjct: 144 DPTTGKHKGYGFIEYEKAQSSQDA-------------VSSXNLFDLGGQYLRVGKAVTPP 190
Query: 152 EH--KPYTPG 159
P TPG
Sbjct: 191 XPLLTPATPG 200
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 32.3 bits (72), Expect = 0.86, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 89 MPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLD 125
M +D + + G+CF+EY + +AE A NG +LD
Sbjct: 71 MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD 107
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 32.3 bits (72), Expect = 0.92, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 92 DPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLD 125
D ++++S G+ F+ + +A+ AKE+ NG +LD
Sbjct: 81 DQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 114
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 92 DPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLDRAHI 129
D ++++S G+ F+ + +A+ AKE+ NG +LD I
Sbjct: 50 DQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 92 DPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLDRAHI 129
D ++++S G+ F+ + +A+ AKE+ NG +LD I
Sbjct: 50 DQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 92 DPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLDRAHI 129
D ++++S G+ F+ + +A+ AKE+ NG +LD I
Sbjct: 47 DQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 13/60 (21%)
Query: 92 DPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLDRAHIFAVNMFDDFDKFMKVPDEWAPP 151
DP T K GY FIEY Q ++ A + ++N+FD ++++V PP
Sbjct: 145 DPTTGKHKGYGFIEYEKAQSSQDA-------------VSSMNLFDLGGQYLRVGKAVTPP 191
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 73 EKFEKLEGVIKEDGLWMPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
E F ++E + + +D ET +S GY FI ++ + A+ A E+ NG++L
Sbjct: 48 EPFGRIESI------QLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFEL 93
>pdb|3OW8|A Chain A, Crystal Structure Of The Wd Repeat-Containing Protein 61
pdb|3OW8|B Chain B, Crystal Structure Of The Wd Repeat-Containing Protein 61
pdb|3OW8|C Chain C, Crystal Structure Of The Wd Repeat-Containing Protein 61
pdb|3OW8|D Chain D, Crystal Structure Of The Wd Repeat-Containing Protein 61
Length = 321
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 43/96 (44%), Gaps = 19/96 (19%)
Query: 204 WTESFVQWSPLGTYLAT-VHRQGAAVWG---GANTFNRLMRYAHPQVKLIDFSPGEKYLV 259
WT +F SP YLAT H ++G G ++ R + I +SP KYL
Sbjct: 126 WTLAF---SPDSQYLATGTHVGKVNIFGVESGKKEYSLDTRGKF--ILSIAYSPDGKYL- 179
Query: 260 TYSSHEPSNPRDANRVVINIFDVRTGKVMRDFKGSA 295
S D +INIFD+ TGK++ +G A
Sbjct: 180 ------ASGAIDG---IINIFDIATGKLLHTLEGHA 206
>pdb|1IRX|A Chain A, Crystal Structure Of Class I Lysyl-Trna Synthetase
pdb|1IRX|B Chain B, Crystal Structure Of Class I Lysyl-Trna Synthetase
Length = 523
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 9/94 (9%)
Query: 118 KTNGYKLDRAHIFAVNMFDDFDKFMKVPDEWAPPEHKPYTP---GENLQKWLTDEKARDQ 174
+ GY++ H M+DD+D+F KVP P E K Y E W E +
Sbjct: 53 RDKGYEVRHIH-----MWDDYDRFRKVPRN-VPQEWKDYLGMPISEVPDPWGCHESYAEH 106
Query: 175 FVIRSGTDTEVLWNDARHLKPEPVYKRSYWTESF 208
F+ + + E L + L +YKR ++E
Sbjct: 107 FMRKFEEEVEKLGIEVDLLYASELYKRGEYSEEI 140
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 83 KEDGLWMPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
K D + + D +T +S GY FI ++ + A A E+ NG++L
Sbjct: 31 KIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFEL 72
>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 = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 13/81 (16%)
Query: 56 SGFGNIIV------VDNLPVVPKEKFEKLEGVIKEDGLWMPVDPETQKSLGYCFIEYNTP 109
SG GNI + +DN + + F + L V + S GY F+ + T
Sbjct: 96 SGVGNIFIKNLDKSIDNKALY--DTFSAFGNI-----LSCKVVCDENGSKGYGFVHFETQ 148
Query: 110 QEAELAKEKTNGYKLDRAHIF 130
+ AE A EK NG L+ +F
Sbjct: 149 EAAERAIEKMNGMLLNDRKVF 169
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 87 LWMPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
+ + +D T S GY +EY T ++A AKE NG ++
Sbjct: 102 IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI 139
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 87 LWMPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
+ +P+D ET+K G+ F+E+ ++A A + N +L
Sbjct: 42 IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 79
>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 = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 13/81 (16%)
Query: 56 SGFGNIIV------VDNLPVVPKEKFEKLEGVIKEDGLWMPVDPETQKSLGYCFIEYNTP 109
SG GNI + +DN + + F + L V + S GY F+ + T
Sbjct: 101 SGVGNIFIKNLDKSIDNKALY--DTFSAFGNI-----LSCKVVCDENGSKGYGFVHFETQ 153
Query: 110 QEAELAKEKTNGYKLDRAHIF 130
+ AE A EK NG L+ +F
Sbjct: 154 EAAERAIEKMNGMLLNDRKVF 174
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 30.0 bits (66), Expect = 4.6, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 89 MPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
+P+D ET+K G+ F+E+ ++A A + N +L
Sbjct: 95 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 130
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 30.0 bits (66), Expect = 4.7, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 94 ETQKSLGYCFIEYNTPQEAELAKEKTNGYKLD 125
+ + + G+CF+EY + +AE A NG +LD
Sbjct: 54 KMKTACGFCFVEYYSRADAENAMRYINGTRLD 85
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 30.0 bits (66), Expect = 5.1, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 98 SLGYCFIEYNTPQEAELAKEKTNGYKLDRAHIF 130
S GY F+ + T + AE A EK NG L+ +F
Sbjct: 44 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 76
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 29.6 bits (65), Expect = 5.3, Method: Composition-based stats.
Identities = 10/28 (35%), Positives = 20/28 (71%)
Query: 98 SLGYCFIEYNTPQEAELAKEKTNGYKLD 125
S+G+ F+EY P++A+ A ++ G+ +D
Sbjct: 49 SMGFGFVEYKKPEQAQKALKQLQGHTVD 76
>pdb|1EFH|A Chain A, Crystal Structure Of The Human Hydroxysteroid
Sulfotransferase In The Presence Of Pap
pdb|1EFH|B Chain B, Crystal Structure Of The Human Hydroxysteroid
Sulfotransferase In The Presence Of Pap
Length = 292
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 18/67 (26%)
Query: 167 TDEKARDQFVIR-----------SGTD--TEVLW-----NDARHLKPEPVYKRSYWTESF 208
T K RD+FVIR SGT+ E+L DA+ ++ P+++RS W ES
Sbjct: 22 TLRKVRDEFVIRDEDVIILTYPKSGTNWLAEILCLMHSKGDAKWIQSVPIWERSPWVESE 81
Query: 209 VQWSPLG 215
+ ++ L
Sbjct: 82 IGYTALS 88
>pdb|1V9D|A Chain A, Crystal Structure Of The Core Fh2 Domain Of Mouse Mdia1
pdb|1V9D|B Chain B, Crystal Structure Of The Core Fh2 Domain Of Mouse Mdia1
pdb|1V9D|C Chain C, Crystal Structure Of The Core Fh2 Domain Of Mouse Mdia1
pdb|1V9D|D Chain D, Crystal Structure Of The Core Fh2 Domain Of Mouse Mdia1
Length = 340
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 26/61 (42%)
Query: 106 YNTPQEAELAKEKTNGYKLDRAHIFAVNMFDDFDKFMKVPDEWAPPEHKPYTPGENLQKW 165
+N +L K+ K+ H A +D + +K PDE A E ENLQK
Sbjct: 159 FNISFLCKLRDTKSADQKMTLLHFLAELCENDHPEVLKFPDELAHVEKASRVSAENLQKS 218
Query: 166 L 166
L
Sbjct: 219 L 219
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 29.6 bits (65), Expect = 5.9, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 98 SLGYCFIEYNTPQEAELAKEKTNGYKLDRAHIF 130
S GY F+ + T + AE A EK NG L+ +F
Sbjct: 50 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 82
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 98 SLGYCFIEYNTPQEAELAKEKTNGYKLDRAHIFAVNMF 135
S GY ++E+ P EAE A + +G ++D I A +
Sbjct: 46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL 83
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 29.6 bits (65), Expect = 6.2, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 89 MPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
+P+D ET+K G+ F+E+ ++A A + N +L
Sbjct: 39 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 74
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 29.3 bits (64), Expect = 6.8, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 89 MPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
+P+D ET+K G+ F+E+ ++A A + N +L
Sbjct: 34 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 69
>pdb|3OBV|E Chain E, Autoinhibited Formin Mdia1 Structure
pdb|3OBV|F Chain F, Autoinhibited Formin Mdia1 Structure
pdb|3OBV|G Chain G, Autoinhibited Formin Mdia1 Structure
pdb|3OBV|H Chain H, Autoinhibited Formin Mdia1 Structure
Length = 457
Score = 29.3 bits (64), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 26/61 (42%)
Query: 106 YNTPQEAELAKEKTNGYKLDRAHIFAVNMFDDFDKFMKVPDEWAPPEHKPYTPGENLQKW 165
+N +L K+ K+ H A +D + +K PDE A E ENLQK
Sbjct: 230 FNISFLCKLRDTKSADQKMTLLHFLAELCENDHPEVLKFPDELAHVEKASRVSAENLQKS 289
Query: 166 L 166
L
Sbjct: 290 L 290
>pdb|3O4X|E Chain E, Crystal Structure Of Complex Between Amino And Carboxy
Terminal Fragments Of Mdia1
pdb|3O4X|H Chain H, Crystal Structure Of Complex Between Amino And Carboxy
Terminal Fragments Of Mdia1
pdb|3O4X|G Chain G, Crystal Structure Of Complex Between Amino And Carboxy
Terminal Fragments Of Mdia1
pdb|3O4X|F Chain F, Crystal Structure Of Complex Between Amino And Carboxy
Terminal Fragments Of Mdia1
Length = 467
Score = 29.3 bits (64), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 26/61 (42%)
Query: 106 YNTPQEAELAKEKTNGYKLDRAHIFAVNMFDDFDKFMKVPDEWAPPEHKPYTPGENLQKW 165
+N +L K+ K+ H A +D + +K PDE A E ENLQK
Sbjct: 249 FNISFLCKLRDTKSADQKMTLLHFLAELCENDHPEVLKFPDELAHVEKASRVSAENLQKS 308
Query: 166 L 166
L
Sbjct: 309 L 309
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 29.3 bits (64), Expect = 6.9, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 89 MPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
+P+D ET+K G+ F+E+ ++A A + N +L
Sbjct: 37 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 72
>pdb|4IFB|A Chain A, Crystal Structure Of Sult 2a1 Llgg Mutant With Paps
pdb|4IFB|B Chain B, Crystal Structure Of Sult 2a1 Llgg Mutant With Paps
Length = 285
Score = 29.3 bits (64), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 18/67 (26%)
Query: 167 TDEKARDQFVIR-----------SGTD--TEVLW-----NDARHLKPEPVYKRSYWTESF 208
T K RD+FVIR SGT+ E+L DA+ ++ P+++RS W ES
Sbjct: 22 TLRKVRDEFVIRDEDVIILTYPKSGTNWLAEILCLMHSKGDAKWIQSVPIWERSPWVESE 81
Query: 209 VQWSPLG 215
+ ++ L
Sbjct: 82 IGYTALS 88
>pdb|3F3Y|A Chain A, Crystal Structure Of Human Cytosolic Sulfotransferase
Sult2a1 In Complex With Pap And Lithocholic Acid
pdb|3F3Y|B Chain B, Crystal Structure Of Human Cytosolic Sulfotransferase
Sult2a1 In Complex With Pap And Lithocholic Acid
pdb|3F3Y|C Chain C, Crystal Structure Of Human Cytosolic Sulfotransferase
Sult2a1 In Complex With Pap And Lithocholic Acid
pdb|3F3Y|D Chain D, Crystal Structure Of Human Cytosolic Sulfotransferase
Sult2a1 In Complex With Pap And Lithocholic Acid
Length = 285
Score = 29.3 bits (64), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 18/67 (26%)
Query: 167 TDEKARDQFVIR-----------SGTD--TEVLW-----NDARHLKPEPVYKRSYWTESF 208
T K RD+FVIR SGT+ E+L DA+ ++ P+++RS W ES
Sbjct: 22 TLRKVRDEFVIRDEDVIILTYPKSGTNWLAEILCLMHSKGDAKWIQSVPIWERSPWVESE 81
Query: 209 VQWSPLG 215
+ ++ L
Sbjct: 82 IGYTALS 88
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 29.3 bits (64), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 91 VDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKLD 125
D ET S G+ F+++N+ ++A+ AKE ++D
Sbjct: 46 TDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID 80
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 87 LWMPVDPETQKSLGYCFIEYNTPQEAELAKEKTNGYKL 124
+ + +D T S GY +EY T ++A AKE NG ++
Sbjct: 56 IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI 93
>pdb|1J99|A Chain A, Crystal Structure Of Human Dehydroepiandrosterone
Sulfotransferase In Complex With Substrate
Length = 293
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 18/67 (26%)
Query: 167 TDEKARDQFVIR-----------SGTD--TEVLW-----NDARHLKPEPVYKRSYWTESF 208
T K RD+FVIR SGT+ E+L DA+ ++ P+++RS W ES
Sbjct: 30 TLRKVRDEFVIRDEDVIILTYPKSGTNWLAEILCLMHSKGDAKWIQSVPIWERSPWVESE 89
Query: 209 VQWSPLG 215
+ ++ L
Sbjct: 90 IGYTALS 96
>pdb|2QP3|A Chain A, Identification And Characterization Of Two Amino Acids
Critical For The Substrate Inhibition Of Sult2a1
Length = 284
Score = 29.3 bits (64), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 18/67 (26%)
Query: 167 TDEKARDQFVIR-----------SGTD--TEVLW-----NDARHLKPEPVYKRSYWTESF 208
T K RD+FVIR SGT+ E+L DA+ ++ P+++RS W ES
Sbjct: 21 TLRKVRDEFVIRDEDVIILTYPKSGTNWLAEILCLMHSKGDAKWIQSVPIWERSPWVESE 80
Query: 209 VQWSPLG 215
+ ++ L
Sbjct: 81 IGYTALS 87
>pdb|1OV4|A Chain A, Crystal Structure Of Human Dhea-st Complexed With
Androsterone
Length = 293
Score = 29.3 bits (64), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 18/67 (26%)
Query: 167 TDEKARDQFVIR-----------SGTD--TEVLW-----NDARHLKPEPVYKRSYWTESF 208
T K RD+FVIR SGT+ E+L DA+ ++ P+++RS W ES
Sbjct: 30 TLRKVRDEFVIRDEDVIILTYPKSGTNWLAEILCLMHSKGDAKWIQSVPIWERSPWVESE 89
Query: 209 VQWSPLG 215
+ ++ L
Sbjct: 90 IGYTALS 96
>pdb|2QP4|A Chain A, Identification And Characterization Of Two Amino Acids
Critical For The Substrate Inhibition Of Sult2a1
Length = 284
Score = 29.3 bits (64), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 18/67 (26%)
Query: 167 TDEKARDQFVIR-----------SGTD--TEVLW-----NDARHLKPEPVYKRSYWTESF 208
T K RD+FVIR SGT+ E+L DA+ ++ P+++RS W ES
Sbjct: 21 TLRKVRDEFVIRDEDVIILTYPKSGTNWLAEILCLMHSKGDAKWIQSVPIWERSPWVESE 80
Query: 209 VQWSPLG 215
+ ++ L
Sbjct: 81 IGYTALS 87
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.135 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,603,720
Number of Sequences: 62578
Number of extensions: 958202
Number of successful extensions: 2573
Number of sequences better than 100.0: 59
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 2518
Number of HSP's gapped (non-prelim): 72
length of query: 702
length of database: 14,973,337
effective HSP length: 106
effective length of query: 596
effective length of database: 8,340,069
effective search space: 4970681124
effective search space used: 4970681124
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: 55 (25.8 bits)