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= 008117
(577 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
V+VG I A + + + G V S++ G PKG+GFCE++ E L A+R L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 191 NKFNIDGQELMLKVDQATRE 210
N G+ L+VD A E
Sbjct: 71 NGREFSGR--ALRVDNAASE 88
>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 = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
++YV + D + SV + G +KS A+ P+ G KG+GF E+E A+ A+
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 190 LNKFNIDGQEL 200
+N F++ GQ L
Sbjct: 187 MNLFDLGGQYL 197
Score = 32.0 bits (71), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 30/72 (41%)
Query: 129 TKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALR 188
++VYVG I D + G +KS + KGF F E+E E AL
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 189 LLNKFNIDGQEL 200
+N + G+ +
Sbjct: 89 QMNSVMLGGRNI 100
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
++YV + D + SV + G +KS A+ P+ G KG+GF E+E A+ A+
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 190 LNKFNIDGQEL 200
+N F++ GQ L
Sbjct: 172 MNLFDLGGQYL 182
Score = 32.0 bits (71), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 29/71 (40%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
+VYVG I D + G +KS + KGF F E+E E AL
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 190 LNKFNIDGQEL 200
+N + G+ +
Sbjct: 75 MNSVMLGGRNI 85
>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 = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
++YV + D + SV + G +KS A+ P+ G KG+GF E+E A+ A+
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 190 LNKFNIDGQEL 200
N F++ GQ L
Sbjct: 171 XNLFDLGGQYL 181
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 28/71 (39%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
+VYVG I D + G +KS + KGF F E+E E AL
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 190 LNKFNIDGQEL 200
N + G+ +
Sbjct: 74 XNSVXLGGRNI 84
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 34/71 (47%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
++YVG + D + + + G ++S + G KG+GF F +E +AL
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 190 LNKFNIDGQEL 200
LN F + G+ +
Sbjct: 88 LNGFELAGRPM 98
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 37.0 bits (84), Expect = 0.032, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 166 NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ 206
NG KG G +FES E RA R++N + G+E+ +++D+
Sbjct: 41 NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR 81
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.0 bits (84), Expect = 0.032, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 166 NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQ 206
NG KG G +FES E RA R++N + G+E+ +++D+
Sbjct: 44 NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR 84
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.0 bits (84), Expect = 0.033, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWK---RAQYPSNGTPKGFGFCEFESAEG 182
KP TKV++G++ D ++ + G +K +P KG+ + EFE+ +
Sbjct: 3 KP-TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPH--LSKGYAYVEFENPDE 59
Query: 183 VLRALRLLNKFNIDGQEL 200
+AL+ ++ IDGQE+
Sbjct: 60 AEKALKHMDGGQIDGQEI 77
>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 = 36.2 bits (82), Expect = 0.053, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 32/74 (43%)
Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
P VY+G I + +L + G V + K P G KG+ F EF E A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 187 LRLLNKFNIDGQEL 200
+R LN + + + L
Sbjct: 62 VRNLNGYQLGSRFL 75
>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 = 36.2 bits (82), Expect = 0.058, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 32/74 (43%)
Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
P VY+G I + +L + G V + K P G KG+ F EF E A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 187 LRLLNKFNIDGQEL 200
+R LN + + + L
Sbjct: 63 VRNLNGYQLGSRFL 76
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 35.8 bits (81), Expect = 0.062, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 32/74 (43%)
Query: 127 PQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRA 186
P VY+G I + +L + G V + K P G KG+ F EF E A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 187 LRLLNKFNIDGQEL 200
+R LN + + + L
Sbjct: 61 VRNLNGYQLGSRFL 74
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 35.4 bits (80), Expect = 0.083, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 32/70 (45%)
Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
+YVG + D + + + G + + + G KG+GF F +E RAL L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 191 NKFNIDGQEL 200
N F + G+ +
Sbjct: 68 NGFELAGRPM 77
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 38/74 (51%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
K+++G + + D V +L G +K++ + + G KG+ FCE+ +A+
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 190 LNKFNIDGQELMLK 203
LN + ++L+++
Sbjct: 158 LNGMQLGDKKLLVQ 171
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 38/74 (51%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
K+++G + + D V +L G +K++ + + G KG+ FCE+ +A+
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 190 LNKFNIDGQELMLK 203
LN + ++L+++
Sbjct: 156 LNGMQLGDKKLLVQ 169
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 38/74 (51%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
K+++G + + D V +L G +K++ + + G KG+ FCE+ +A+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 190 LNKFNIDGQELMLK 203
LN + ++L+++
Sbjct: 63 LNGMQLGDKKLLVQ 76
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 32.3 bits (72), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 38/74 (51%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
K+++G + + D V +L G +K++ + + G KG+ FCE+ +A+
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 190 LNKFNIDGQELMLK 203
LN + ++L+++
Sbjct: 176 LNGMQLGDKKLLVQ 189
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 32.0 bits (71), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 29/59 (49%)
Query: 149 LKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA 207
+V G +K +G P+G+ F E+E + A + + IDG+ +++ V++
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 29/59 (49%)
Query: 149 LKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKVDQA 207
+V G +K +G P+G+ F E+E + A + + IDG+ +++ V++
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 3/84 (3%)
Query: 126 KPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFE---SAEG 182
K K+++G + D + GTV K + P+ G +GFGF FE S +
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 183 VLRALRLLNKFNIDGQELMLKVDQ 206
V++ +L+ ID + + + +Q
Sbjct: 61 VVKTQHILDGKVIDPKRAIPRDEQ 84
Score = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 130 KVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
K++VG I P GT+ + G +GFGF ++SA+ V R +
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ- 147
Query: 190 LNKFNIDGQELMLKVDQA 207
NKF ID ++ +++ +A
Sbjct: 148 -NKF-IDFKDRKIEIKRA 163
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 31.2 bits (69), Expect = 1.5, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 171 GFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV-DQATR 209
GFGF E++ E +AL+ L +DG +L +++ ++AT+
Sbjct: 51 GFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK 90
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 22/39 (56%)
Query: 166 NGTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELMLKV 204
NG KG+ F EF S E AL NK I+G+ + L++
Sbjct: 49 NGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 128 QTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRAL 187
+ K++VG ++ + + V G + + +GFGF FE+ + A+
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 188 RLLNKFNIDGQELMLKVDQATR 209
+N ++DG++ ++VDQA +
Sbjct: 72 MAMNGKSVDGRQ--IRVDQAGK 91
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%)
Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRL 189
+YVG + A ++ + + CG+V +G PKGF + EF E V +L L
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 66
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 29/65 (44%)
Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVL 184
E +YVG + A ++ + + CG+V +G PKGF + EF E V
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 185 RALRL 189
+L L
Sbjct: 63 TSLAL 67
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 167 GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQELML 202
G+ KGFGF +F S E A + IDG ++ L
Sbjct: 51 GSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL 86
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 29.6 bits (65), Expect = 4.6, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 167 GTPKGFGFCEFESAEGVLRALRLLNKFNIDGQEL 200
G PK FGF F+ E V A+ LLN + G+ +
Sbjct: 54 GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 29.6 bits (65), Expect = 5.1, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 125 EKPQTKVYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAE 181
E+ T +Y+ + + D + ++LK G V S R S+GT +G GF ES E
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARMESTE 77
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 28.9 bits (63), Expect = 7.2, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 131 VYVGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLL 190
+YVG + +A S+ V + G V + K PKGFGF E + E V A+ L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 191 NKFNIDGQEL 200
+ + G+ +
Sbjct: 63 DNTDFMGRTI 72
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 28.9 bits (63), Expect = 7.4, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 31/68 (45%)
Query: 133 VGKIAPTADSDFVLSVLKVCGTVKSWKRAQYPSNGTPKGFGFCEFESAEGVLRALRLLNK 192
V I T D + + + G ++S K +G+GF +F+S +A+ LN
Sbjct: 47 VNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
Query: 193 FNIDGQEL 200
FNI + L
Sbjct: 107 FNILNKRL 114
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 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,907,196
Number of Sequences: 62578
Number of extensions: 357624
Number of successful extensions: 575
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 542
Number of HSP's gapped (non-prelim): 39
length of query: 577
length of database: 14,973,337
effective HSP length: 104
effective length of query: 473
effective length of database: 8,465,225
effective search space: 4004051425
effective search space used: 4004051425
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: 54 (25.4 bits)