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= 001930
(995 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 97.1 bits (240), Expect = 5e-20, Method: Composition-based stats.
Identities = 46/96 (47%), Positives = 68/96 (70%), Gaps = 2/96 (2%)
Query: 104 VRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVY 163
VRV+Q+NLV+++GL LAD ++L+R EYFG++GK+ KV I+ + + S S Y
Sbjct: 10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTS--YAGSQGPSASAY 67
Query: 164 ITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYC 199
+TY R +DA+R IQ V++ ++DGR L+A GTTKYC
Sbjct: 68 VTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC 103
>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
Length = 52
Score = 59.3 bits (142), Expect = 1e-08, Method: Composition-based stats.
Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 9 CPLCAEEMDLTDQQLKPCNCGYEICVWCWNHIMEMAEKDGTEGRCPACRTAYDKE 63
CPLC E +++ D PC CGY+IC +CW+ I + G CPACR Y ++
Sbjct: 3 CPLCMEPLEIDDINFFPCTCGYQICRFCWHRI-----RTDENGLCPACRKPYPED 52
>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4
Length = 78
Score = 58.2 bits (139), Expect = 3e-08, Method: Composition-based stats.
Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 9 CPLCAEEMDLTDQQLKPCNCGYEICVWCWNHIMEMAEKDGTEGRCPACRTAYDKEKIV 66
CPLC E +++ D PC CGY+IC +CW+ I + G CPACR Y ++ V
Sbjct: 14 CPLCMEPLEIDDINFFPCTCGYQICRFCWHRI-----RTDENGLCPACRKPYPEDPAV 66
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 39.7 bits (91), Expect = 0.009, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 8/83 (9%)
Query: 109 RNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSR 168
++ VY+ LP +L + DL + F +YGKV+KV+I + + + + +I +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYR---IFSKYGKVVKVTIMKD-----KDTRKSKGVAFILFLD 67
Query: 169 EDDAIRCIQSVHSYILDGRPLRA 191
+D A C +++++ L GR ++A
Sbjct: 68 KDSAQNCTRAINNKQLFGRVIKA 90
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 37.7 bits (86), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 4 KAEKTCPLCAEEMDLTDQQLKPCNCGYEICVWCW--NHIMEMAEKDGTEGRCPACRTAYD 61
K E TCP+C ++L Q L +CG+ C C NH M +K E CP CR +Y
Sbjct: 17 KEEVTCPIC---LELLTQPLSL-DCGHSFCQACLTANHKKSMLDKG--ESSCPVCRISYQ 70
Query: 62 KEKI 65
E I
Sbjct: 71 PENI 74
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 37.7 bits (86), Expect = 0.033, Method: Composition-based stats.
Identities = 27/109 (24%), Positives = 47/109 (43%), Gaps = 27/109 (24%)
Query: 89 KAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTA 148
K++PK R+H++N+ P D DL ++ FGQ+GK+L V I
Sbjct: 26 KSQPK----RLHVSNI-------------PFRFRDPDL---RQMFGQFGKILDVEIIFNE 65
Query: 149 TGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTK 197
G ++T+ DA R + +H +++GR + T +
Sbjct: 66 RGSKGFG-------FVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 37.4 bits (85), Expect = 0.039, Method: Composition-based stats.
Identities = 35/124 (28%), Positives = 55/124 (44%), Gaps = 19/124 (15%)
Query: 60 YDKEKIVGMAANCERAVARMTSERRQKSQKAKPKPSEGRMHLTNVRVIQRNLVYIIGLPI 119
Y EK+ G+ V ++ S +KS++ EGR + I L
Sbjct: 174 YCVEKLNGLKIEGYTLVTKV-SNPLEKSKRTDSATLEGRE------------IXIRNLST 220
Query: 120 NLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSV 179
L DE+LL +E F +G + K++I G +HS NN CC + + +D A R +Q
Sbjct: 221 ELLDENLL--RESFEGFGSIEKINIP---AGQKEHSFNN-CCAFXVFENKDSAERALQXN 274
Query: 180 HSYI 183
S +
Sbjct: 275 RSLL 278
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.8 bits (81), Expect = 0.13, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 112 VYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDD 171
+++ +P D DL ++ FGQ+GK+L V I G ++T+ D
Sbjct: 18 LHVSNIPFRFRDPDL---RQMFGQFGKILDVEIIFNERGSKGFG-------FVTFENSAD 67
Query: 172 AIRCIQSVHSYILDGRPLRACFGTTK 197
A R + +H +++GR + T +
Sbjct: 68 ADRAREKLHGTVVEGRKIEVNNATAR 93
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 35.4 bits (80), Expect = 0.15, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 114 IIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAI 173
+ GL + + DL +E F +YG + VSI Q S + ++ + DDA
Sbjct: 17 VFGLSLYTTERDL---REVFSKYGPIADVSIVYD-----QQSRRSRGFAFVYFENVDDAK 68
Query: 174 RCIQSVHSYILDGRPLRACFGTTKYCH 200
+ + LDGR +R F TK H
Sbjct: 69 EAKERANGMELDGRRIRVDFSITKRPH 95
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 35.4 bits (80), Expect = 0.15, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 114 IIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAI 173
+ GL + + DL +E F +YG + VSI Q S + ++ + DDA
Sbjct: 51 VFGLSLYTTERDL---REVFSKYGPIADVSIVYD-----QQSRRSRGFAFVYFENVDDAK 102
Query: 174 RCIQSVHSYILDGRPLRACFGTTKYCH 200
+ + LDGR +R F TK H
Sbjct: 103 EAKERANGMELDGRRIRVDFSITKRPH 129
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 34.7 bits (78), Expect = 0.24, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 114 IIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAI 173
+ GL + + DL +E F +YG + VSI Q S + ++ + DDA
Sbjct: 20 VFGLSLYTTERDL---REVFSKYGPIADVSIVYD-----QQSRRSRGFAFVYFENVDDAK 71
Query: 174 RCIQSVHSYILDGRPLRACFGTTKYCH 200
+ + LDGR +R F TK H
Sbjct: 72 EAKERANGMELDGRRIRVDFSITKRPH 98
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 34.3 bits (77), Expect = 0.39, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 4 KAEKTCPLCAEEMDLTDQQLKPCNCGYEICVWCWNHIMEMAEKDGTEGRCPACRTAY 60
K E TCP+C E + ++ +C + C C E +G CP CR Y
Sbjct: 17 KEEVTCPICLELL----KEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPY 69
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 33.5 bits (75), Expect = 0.66, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 4 KAEKTCPLCAEEMDLTDQQLKPCNCGYEICVWCWNHIMEMAEKDGTEGRCPACRTAYDKE 63
+ E CP+C + + Q+ +CG+ C+ C I ++ E +CP C+T+ K
Sbjct: 18 QEEVICPICLDIL----QKPVTIDCGHNFCLKC---ITQIGETSCGFFKCPLCKTSVRKN 70
Query: 64 KI 65
I
Sbjct: 71 AI 72
>pdb|1X4W|A Chain A, Solution Structure Of The Zf-An1 Domain From Human
Hypothetical Protein Flj13222
Length = 67
Score = 32.0 bits (71), Expect = 1.7, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 4 KAEKTCPLCAEEMDLTDQQLKPCNCGYEICV 34
K+ + C C +++L Q+L C CGY C+
Sbjct: 13 KSRRRCFQCQTKLELVQQELGSCRCGYVFCM 43
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 7/50 (14%)
Query: 9 CPLCAEEMDLTDQQLKP--CNCGYEICVWCWNHIMEMAEKDGTEGRCPAC 56
CP+C E T++QL+P +CG+ IC C ++ + +G RCP C
Sbjct: 18 CPICME--SFTEEQLRPKLLHCGHTICRQCLEKLLA-SSINGV--RCPFC 62
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 30.8 bits (68), Expect = 4.3, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 14/85 (16%)
Query: 113 YIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDA 172
YI +P + DL+ F +G +L D +H CC +I Y + A
Sbjct: 31 YIGNIPHFATEADLI---PLFQNFGFIL----------DFKHYPEKGCC-FIKYDTHEQA 76
Query: 173 IRCIQSVHSYILDGRPLRACFGTTK 197
CI ++ ++ GR LR +G +
Sbjct: 77 AVCIVALANFPFQGRNLRTGWGKER 101
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 30.4 bits (67), Expect = 4.5, Method: Composition-based stats.
Identities = 27/127 (21%), Positives = 54/127 (42%), Gaps = 27/127 (21%)
Query: 75 AVARMTSERRQKSQKAKPKPSEGRMHL------------TNVRVIQRNLVYIIGLPINLA 122
A+AR R + KP P + + L T +++ NL + ++
Sbjct: 48 AIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDF------GVS 101
Query: 123 DEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHSY 182
D D+ +E F ++G + K ++ +G +A+ + + R DA++ ++
Sbjct: 102 DADI---QELFAEFGTLKKAAVDYDRSGRSLGTAD------VHFERRADALKAMKQYKGV 152
Query: 183 ILDGRPL 189
LDGRP+
Sbjct: 153 PLDGRPM 159
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 5.1, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 117 LPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCI 176
L ++D D+ +E F ++G + K ++ +G +A+ + + R DA++ +
Sbjct: 43 LDFGVSDADI---QELFAEFGTLKKAAVDYDRSGRSLGTAD------VHFERRADALKAM 93
Query: 177 QSVHSYILDGRPL 189
+ LDGRP+
Sbjct: 94 KQYKGVPLDGRPM 106
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 5.2, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 117 LPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCI 176
L ++D D+ +E F ++G + K ++ +G +A+ + + R DA++ +
Sbjct: 43 LDFGVSDADI---QELFAEFGTLKKAAVDYDRSGRSLGTAD------VHFERRADALKAM 93
Query: 177 QSVHSYILDGRPL 189
+ LDGRP+
Sbjct: 94 KQYKGVPLDGRPM 106
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.4 bits (67), Expect = 5.4, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 9/73 (12%)
Query: 117 LPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCI 176
L ++D D+ +E F ++G + K ++ +G +A+ + + R+ DA++ +
Sbjct: 36 LDFGVSDADI---QELFAEFGTLKKAAVHYDRSGRSLGTAD------VHFERKADALKAM 86
Query: 177 QSVHSYILDGRPL 189
+ + LDGRP+
Sbjct: 87 KQYNGVPLDGRPM 99
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 29.6 bits (65), Expect = 8.0, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 46/84 (54%), Gaps = 11/84 (13%)
Query: 105 RVIQRNL-VYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVY 163
R +Q+ + ++GLP ++DL KEYF +G+VL V + + D++ + ++ +
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDL---KEYFSTFGEVLMVQVKK----DLK-TGHSKGFGF 61
Query: 164 ITYSREDDAIRCIQSVHSYILDGR 187
+ ++ + ++ + H ++DGR
Sbjct: 62 VRFTEYETQVKVMSQRH--MIDGR 83
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 0.129 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,876,894
Number of Sequences: 62578
Number of extensions: 1167654
Number of successful extensions: 1767
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 1751
Number of HSP's gapped (non-prelim): 38
length of query: 995
length of database: 14,973,337
effective HSP length: 108
effective length of query: 887
effective length of database: 8,214,913
effective search space: 7286627831
effective search space used: 7286627831
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: 56 (26.2 bits)