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= 032280
(144 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSA 117
S D+ LFV L +V + N F++FP Y S H+ Q S+ + F F+ Q A
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 118 LGAMYAL 124
AM ++
Sbjct: 143 QNAMDSM 149
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN 126
++V LP D++ ++I ++F ++ L++ + PFAF F D + A A+Y +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR-RGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 127 FAPSDSACSLLFPHS 141
+ + FP S
Sbjct: 84 YDYDGYRLRVEFPRS 98
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYA 123
LFV L +V + N F++FP Y S H+ Q S+ + F F+ Q A AM +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 124 L 124
+
Sbjct: 63 M 63
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 32.3 bits (72), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 49 GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPF 106
GS +S P + D T+ V L ED + ++ LFR F +L +T S+ F
Sbjct: 1 GSSGSSGPNRRADDNA-TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGF 59
Query: 107 AFAVFSDQQSALGAMYALNNFA 128
AF F ++ A A+ ++ F
Sbjct: 60 AFISFHRREDAARAIAGVSGFG 81
>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 = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
+ LF+ LPE+ + LF +FPG++ L N AF F+ + + A AL
Sbjct: 9 QILFLTNLPEETNEMMLSMLFNQFPGFKEVRL---VPNRHDIAFVEFTTELQSNAAKEAL 65
Query: 125 NNF 127
F
Sbjct: 66 QGF 68
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 31.6 bits (70), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 66 TLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYA 123
T++V+ LP + ++Y +F ++ + T+ S+ AF +F D+ SA A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 124 LNN 126
+NN
Sbjct: 78 INN 80
>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 = 30.8 bits (68), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN 126
LF+ LPE+ + LF +FPG++ L + AF F ++ A A AL
Sbjct: 210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD---IAFVEFDNEVQAGAARDALQG 266
Query: 127 F 127
F
Sbjct: 267 F 267
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 30.4 bits (67), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 116
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151
Query: 117 A 117
Sbjct: 152 V 152
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 30.4 bits (67), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPG-YESSHLRSS-TQNSQPFAFAVFSDQQSA 117
+D ++ LF+ +P ++ +++ LF EF YE + L+ T + AF + +++SA
Sbjct: 10 DHDAIK-LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 118 LGAMYALNN 126
L A AL+
Sbjct: 69 LKAQSALHE 77
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 30.4 bits (67), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 116
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Query: 117 A 117
Sbjct: 159 V 159
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 30.4 bits (67), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 116
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 97 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 156
Query: 117 A 117
Sbjct: 157 V 157
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 30.4 bits (67), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
LF+ LPE+ + LF +FPG++ L + AF F ++ A A AL
Sbjct: 15 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD---IAFVEFDNEVQAGAARDALQ 71
Query: 126 NF 127
F
Sbjct: 72 GF 73
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 116
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 100 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 159
Query: 117 A 117
Sbjct: 160 V 160
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 116
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Query: 117 A 117
Sbjct: 159 V 159
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 30.0 bits (66), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 124
L+V L ++ + +F F ES L S T S+ + F FSD + A A+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 125 NNF 127
N F
Sbjct: 89 NGF 91
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.0 bits (66), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYAL 124
L V LP+D+ RE+Y LFR + + T S +AF F+ + + A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 125 NNFAPSDSACSL 136
N + +
Sbjct: 66 NGITVRNKRLKV 77
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 30.0 bits (66), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 116
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 98 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 157
Query: 117 A 117
Sbjct: 158 V 158
>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 = 29.3 bits (64), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 124
L+V+GLP+ + +E+ LF ++ +S + T S+ F F + A A+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 125 NNFAPS 130
N PS
Sbjct: 151 NGQKPS 156
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 29.3 bits (64), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYAL 124
L V LP+D+ RE+Y LFR + + T S +AF F+ + + A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 125 NNFAPSDSACSL 136
N + +
Sbjct: 66 NGITVRNKRLKV 77
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 29.3 bits (64), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 66 TLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMYA 123
L+V+GLP+ + +E+ LF ++ +S L +T S+ F F + A A+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 124 LNNFAPSDSA 133
LN P +A
Sbjct: 63 LNGQKPLGAA 72
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
L+V+GLP+ + +E+ LF ++ +S L +T S+ F F + A A+ L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 125 NNFAP 129
N P
Sbjct: 153 NGQKP 157
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 13/82 (15%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSA------- 117
+FV G+P + E+ F++F + + +P F F F D+QS
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 118 ----LGAMYALNNFAPSDSACS 135
+G + P DS S
Sbjct: 73 FHDIMGKKVEVKRAEPRDSKSS 94
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQSALGAMY 122
+TLFV GL ED L F G + + + T +S+ F F F+ ++ A A
Sbjct: 16 KTLFVKGLSEDTTEE---TLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 123 ALNN 126
A+ +
Sbjct: 73 AMED 76
>pdb|2WB9|A Chain A, Fasciola Hepatica Sigma Class Gst
pdb|2WB9|B Chain B, Fasciola Hepatica Sigma Class Gst
pdb|2WDU|A Chain A, Fasciola Hepatica Sigma Class Gst
pdb|2WDU|B Chain B, Fasciola Hepatica Sigma Class Gst
Length = 211
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 52 SASFPAYGSYDEVRTLF--VAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFA 109
+ F G DE L + G ED+ RE+Y +FR G + + ++ +N+ P
Sbjct: 79 ARQFKMMGETDEEYYLIERIIGECEDLY-REVYTIFRTPQGEKEAKIKEFKENNGPTLLK 137
Query: 110 VFSDQQSALGAMYALNN 126
+ S+ + G + N
Sbjct: 138 LVSESLESSGGKHVAGN 154
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 124
LFV GL D + + +F ++ + TQ S+ F F F + A AM A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 125 N 125
N
Sbjct: 75 N 75
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREF 88
R +FV GLP D+ EI FR F
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRF 32
>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 = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPF--AFAVFSDQQSALGAMYAL 124
L V LP+D RE+Y LFR + + + F AF F+ + + A+ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 125 NNFAPSDSACSL 136
N + +
Sbjct: 77 NGITVRNKRLKV 88
>pdb|2YV5|A Chain A, Crystal Structure Of Yjeq From Aquifex Aeolicus
Length = 302
Score = 27.7 bits (60), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 49 GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH 95
GS+ P + + T+FV KPRE+ N FREF Y+ +
Sbjct: 217 GSFVGDTPGFSKVEA--TMFV-------KPREVRNYFREFLRYQCKY 254
>pdb|4EO3|A Chain A, Peroxiredoxin Nitroreductase Fusion Enzyme
pdb|4EO3|B Chain B, Peroxiredoxin Nitroreductase Fusion Enzyme
Length = 322
Score = 27.3 bits (59), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 71 GLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQ 115
L +D PRE L +++HL S N+QP+ F V +++
Sbjct: 156 ALKKDRVPREELELL-----IKAAHLAPSCMNNQPWRFVVVDEEE 195
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
R L++ LP + E+Y++F ++ + +T ++ A+ V+ D A A+ L
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRV-GNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 125 NNFAPSDSACSLLF 138
+ F S+ +L+
Sbjct: 68 SGFNVSNRYLVVLY 81
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYAL 124
LFV G+ E+ +I++ F E+ ++ HL + + + + + A AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 125 N 125
N
Sbjct: 70 N 70
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYAL 124
LFV G+ E+ +I++ F E+ ++ HL + + + + + A AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 125 N 125
N
Sbjct: 70 N 70
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYAL 124
LFV G+ E+ +I++ F E+ ++ HL + + + + + A AM L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 125 N 125
N
Sbjct: 72 N 72
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 27.3 bits (59), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYAL 124
LFV G+ E+ +I++ F E+ ++ HL + + + + + A AM L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 125 N 125
N
Sbjct: 70 N 70
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYAL 124
LFV G+ E+ +I++ F E+ ++ HL + + + + + A AM L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 125 N 125
N
Sbjct: 85 N 85
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 49 GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPG-YESSHLRSS-TQNSQPF 106
GS +S +D ++ LFV +P + +++ LF EF YE + L+ T +
Sbjct: 1 GSSGSSGVPMKDHDAIK-LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGC 59
Query: 107 AFAVFSDQQSALGAMYALNN 126
AF + + SAL A AL+
Sbjct: 60 AFLTYCARDSALKAQSALHE 79
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYAL 124
LFV G+ E+ +I++ F E+ ++ HL + + + + + A AM L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 125 N 125
N
Sbjct: 86 N 86
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 3/74 (4%)
Query: 55 FPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREF-PGYESSHLRSSTQNSQPFAFAVFSD 113
FPA D RT+FV L V+ +Y LF + P + + + + F F F
Sbjct: 9 FPAQEEAD--RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKH 66
Query: 114 QQSALGAMYALNNF 127
+S A+ LN
Sbjct: 67 PESVSYAIALLNGI 80
>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 = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFS 112
D+ +FV G+ DV+P+E F ++ + L T S+ F F +
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 26.9 bits (58), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 67 LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 124
L+V L ++ + +F F ++ L S T S+ + F FSD + A A+ L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 125 NNF 127
N F
Sbjct: 68 NGF 70
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 122
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 123 ALN 125
+N
Sbjct: 124 NMN 126
>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 = 26.6 bits (57), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 122
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 123 ALN 125
+N
Sbjct: 68 NMN 70
>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 = 26.6 bits (57), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 122
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 123 ALN 125
+N
Sbjct: 63 NMN 65
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 26.6 bits (57), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 122
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 123 ALN 125
+N
Sbjct: 66 NMN 68
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 26.2 bits (56), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 122
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 123 ALN 125
+N
Sbjct: 73 NMN 75
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 26.2 bits (56), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
R L++ LP + E+Y++F ++ + +T ++ A+ V+ D A A L
Sbjct: 13 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRV-GNTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 125 NNFAPSDSACSLLF 138
+ F + +L+
Sbjct: 72 SGFNVCNRYLVVLY 85
>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 = 26.2 bits (56), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 2/73 (2%)
Query: 62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALG 119
D LF+ GLP + ++ L F ++ +L S+T S+ +AF + D
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 120 AMYALNNFAPSDS 132
A+ LN D
Sbjct: 172 AIAGLNGMQLGDK 184
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
0.319 0.134 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,662,324
Number of Sequences: 62578
Number of extensions: 104266
Number of successful extensions: 315
Number of sequences better than 100.0: 58
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 46
Number of HSP's that attempted gapping in prelim test: 302
Number of HSP's gapped (non-prelim): 58
length of query: 144
length of database: 14,973,337
effective HSP length: 89
effective length of query: 55
effective length of database: 9,403,895
effective search space: 517214225
effective search space used: 517214225
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)