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= 029268
(196 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 111 bits (277), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 51/87 (58%), Positives = 65/87 (74%), Gaps = 1/87 (1%)
Query: 64 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQ 122
E D+RS++VGNVDY T EE++ HF CG+VNRVTI DKF G PKG+AY+EF E+V+
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 123 EALHLNESELHGRQLKVTVKRTNVPGM 149
+L L+ES GRQ+KV KRTN PG+
Sbjct: 62 TSLALDESLFRGRQIKVIPKRTNRPGI 88
>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 = 110 bits (276), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 51/87 (58%), Positives = 65/87 (74%), Gaps = 1/87 (1%)
Query: 64 EVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQ 122
E D+RS++VGNVDY T EE++ HF CG+VNRVTI DKF G PKG+AY+EF E+V+
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 123 EALHLNESELHGRQLKVTVKRTNVPGM 149
+L L+ES GRQ+KV KRTN PG+
Sbjct: 63 TSLALDESLFRGRQIKVIPKRTNRPGI 89
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 108 bits (270), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 47/93 (50%), Positives = 68/93 (73%), Gaps = 1/93 (1%)
Query: 58 SLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFL 116
S ++E+D RSV+VGNVDY T ++++ HF SCG++NR+TI DKF G PKGYAY+EF
Sbjct: 27 SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA 86
Query: 117 QSEAVQEALHLNESELHGRQLKVTVKRTNVPGM 149
+ +V A+ ++E+ GR +KV KRTN+PG+
Sbjct: 87 ERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGI 119
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 53.9 bits (128), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 49/75 (65%), Gaps = 3/75 (4%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL- 125
R+++VGN+ YS T E+V++ F G V V + D+ +PKG+ +VE +Q E+V EA+
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 126 HLNESELHGRQLKVT 140
L+ ++ GR ++VT
Sbjct: 61 KLDNTDFMGRTIRVT 75
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL- 125
RSVFVGN+ Y T E+++ F G V + D+ G+PKGY + E+ E A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 126 HLNESELHGRQLKV 139
+LN E GR L+V
Sbjct: 69 NLNGREFSGRALRV 82
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 47/80 (58%), Gaps = 2/80 (2%)
Query: 62 REEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 121
+EE D R+VFVGN++ E + + F G + +VTI D+ G+PK + +V F E+V
Sbjct: 12 QEEAD-RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70
Query: 122 QEALH-LNESELHGRQLKVT 140
A+ LN L+GR + V+
Sbjct: 71 SYAIALLNGIRLYGRPINVS 90
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 128
+VFVG +D E++ F G+V V I TD+ G KGY +V F VQ+ + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-S 69
Query: 129 ESELHGRQLKV 139
+ HG++LK+
Sbjct: 70 QINFHGKKLKL 80
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 128
+VFVG +D E++ F G+V V I TD+ G KGY +V F VQ+ + +
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-S 70
Query: 129 ESELHGRQLKV 139
+ HG++LK+
Sbjct: 71 QINFHGKKLKL 81
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 128
+VFVG +D E++ F G+V V I TD+ G KGY +V F VQ+ + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-S 69
Query: 129 ESELHGRQLKV 139
+ HG++LK+
Sbjct: 70 QINFHGKKLKL 80
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 35/106 (33%), Positives = 49/106 (46%), Gaps = 1/106 (0%)
Query: 53 AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 112
+ GSS A + +VFV N+DY +++++ F G V R I DK G+ +G
Sbjct: 1 GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGT 60
Query: 113 VEFLQS-EAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRP 157
V F QS EAVQ N L R + V + +P P RP
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERP 106
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 4/78 (5%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 127
R ++VGN+D + T + ++Q+FQ G + + I DK + YA+VE+ QS AL
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ- 59
Query: 128 NESELHGRQLKVTVKRTN 145
L+G+Q++ + + N
Sbjct: 60 ---TLNGKQIENNIVKIN 74
>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 = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 65 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF-LQSEAVQE 123
++ +F+ + +SCT EE+++ ++ GTV + + T++ G+PKG AYVE+ +S+A Q
Sbjct: 15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQA 74
Query: 124 ALHLNESELHGRQLKVTVKRT 144
+ ++ + +KV + +
Sbjct: 75 VMKMDGMTIKENIIKVAISNS 95
>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 = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 52/95 (54%), Gaps = 10/95 (10%)
Query: 51 DPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPKG 109
DP A G + +++FV V+Y T ++++ F+ G + R+ + + + G+P+G
Sbjct: 94 DPNAQGDAF--------KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 110 YAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 143
YA++E+ + A H + ++ GR++ V V+R
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>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 = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 52/96 (54%), Gaps = 10/96 (10%)
Query: 50 QDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRV-TIRTDKFGQPK 108
DP A G + +++FV V+Y T ++++ F+ G + R+ + + + G+P+
Sbjct: 93 NDPNAQGDAF--------KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPR 144
Query: 109 GYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 143
GYA++E+ + A H + ++ GR++ V V+R
Sbjct: 145 GYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 48/78 (61%), Gaps = 4/78 (5%)
Query: 66 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 125
+S+++ + N+ YS T E +Q+ F+ + + ++ G+ KGYA++EF E +EAL
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 126 H-LNESELHGRQLKVTVK 142
+ N+ E+ GR +++ ++
Sbjct: 71 NSCNKREIEGRAIRLELQ 88
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEALHLN 128
+FVG + ++C E++++F+ G V V + D Q P+G+ ++ F ++V +A++++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 129 ESELHGRQLKVTVKRT 144
++ G+ KV VKR
Sbjct: 73 FHDIMGK--KVEVKRA 86
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 60 ANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQS 118
A++ E D+ FVG + + + ++++ +F G V TI+ D G+ +G+ ++ F +
Sbjct: 4 ASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDA 63
Query: 119 EAVQEALHLNESELHGRQL 137
+V++ L E L GR +
Sbjct: 64 ASVEKVLDQKEHRLDGRVI 82
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALH- 126
+V+V N+ +S T ++ + F G V +VTI DK + KG A++ FL ++ Q
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 127 LNESELHGRQLKVTV 141
+N +L GR +K ++
Sbjct: 78 INNKQLFGRVIKASI 92
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLN 128
+F+G + + T ++++ +F G V T++ D G+ +G+ +V F +SE+V + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 129 ESELHGRQL 137
E +L+G+ +
Sbjct: 62 EHKLNGKVI 70
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 63 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAV 121
EE D+R+VF + P +++ F + G V V I +D+ + KG AYVEF + ++V
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 122 QEALHLNESELHG 134
A+ L L G
Sbjct: 81 PLAIGLTGQRLLG 93
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 48/105 (45%), Gaps = 7/105 (6%)
Query: 56 GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVE 114
GSS ++ + VFVG++ T E+++ F G ++ + D G+ KGY +V
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVS 63
Query: 115 FLQSEAVQEAL-HLNESELHGRQLKVTVKRTNVPGMKQHRPRRPN 158
F + A+ H+ L GRQ+ RTN K P P+
Sbjct: 64 FYNKLDAENAIVHMGGQWLGGRQI-----RTNWATRKPPAPSGPS 103
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEAL-HL 127
V+VG++ Y + ++Q F G + + + D + KG+A+VE+ EA Q AL +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 128 NESELHGRQLKV 139
N L GR +KV
Sbjct: 91 NSVMLGGRNIKV 102
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 49/91 (53%), Gaps = 4/91 (4%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HL 127
++V +V + ++++ F++ G + T+ D G+ KGY ++E+ ++++ Q+A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 128 NESELHGRQLKVTVKRTNVPGMKQHRPRRPN 158
N +L G+ L+ V + P M P P
Sbjct: 188 NLFDLGGQYLR--VGKAVTPPMPLLTPATPG 216
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 52/105 (49%), Gaps = 10/105 (9%)
Query: 53 AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV--NRVT------IRTDK- 103
+ GSS E+ D+ +++V ++ S T +++ F+ CG V N+ T I DK
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 104 FGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKRTNVP 147
G+PKG A V + + A+ + + G +LKV++ R P
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 53 AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYA 111
+ GSS NR D+ ++ V N+ ++Q+ F+ G+++R+ + DK GQ KG+A
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 112 YVEFLQSEAVQEAL 125
++ F + E A+
Sbjct: 61 FISFHRREDAARAI 74
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEAL-HL 127
V+VG++ Y + ++Q F G + + + D + KG+A+VE+ EA Q AL +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 128 NESELHGRQLKV 139
N L GR +KV
Sbjct: 76 NSVMLGGRNIKV 87
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HL 127
++V +V + ++++ F++ G + T+ D G+ KGY ++E+ ++++ Q+A+ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 128 NESELHGRQLKV 139
N +L G+ L+V
Sbjct: 173 NLFDLGGQYLRV 184
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/115 (23%), Positives = 54/115 (46%), Gaps = 17/115 (14%)
Query: 54 AGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAY 112
G S + +E R +F+G + + T E ++ HF+ GT+ + V +R + +G+ +
Sbjct: 1 GGSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 60
Query: 113 VEFLQSEAVQEALHLNESELHGRQLK----------------VTVKRTNVPGMKQ 151
V + E V A++ ++ GR ++ +TVK+ V G+K+
Sbjct: 61 VTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 115
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 125
+ +FVG + ++ +F+ G + + I TD+ G+ +G+A+V F ++V + +
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 127
R +FVG ++ + E+V + FQ G ++ T+ G KG A+V+F Q A+H
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH- 74
Query: 128 NESELHGRQ 136
LHG Q
Sbjct: 75 ---ALHGSQ 80
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLN 128
+FVG +D+S T E ++ +F G V I DK Q +G+ +V+F V L
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 129 ESELHGRQL 137
L GR +
Sbjct: 79 PHTLDGRNI 87
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 6/76 (7%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIR---TDKFGQPKGYAYVEFLQSEAVQEAL 125
+ +VGN+ ++ ++ F+ + +R TDKF KG+ YVEF + ++++EAL
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKF---KGFCYVEFDEVDSLKEAL 73
Query: 126 HLNESELHGRQLKVTV 141
+ + L R L+V +
Sbjct: 74 TYDGALLGDRSLRVDI 89
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 49/101 (48%), Gaps = 17/101 (16%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 126
R +F+G + + T E ++ HF+ GT+ + V +R + +G+ +V + E V A++
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 127 LNESELHGRQLK----------------VTVKRTNVPGMKQ 151
++ GR ++ +TVK+ V G+K+
Sbjct: 74 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 114
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 125
+ +FVG + ++ +F+ G + + I TD+ G+ +G+A+V F ++V + +
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 49/101 (48%), Gaps = 17/101 (16%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 126
R +F+G + + T E ++ HF+ GT+ + V +R + +G+ +V + E V A++
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 127 LNESELHGRQLK----------------VTVKRTNVPGMKQ 151
++ GR ++ +TVK+ V G+K+
Sbjct: 67 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 107
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 125
+ +FVG + ++ +F+ G + + I TD+ G+ +G+A+V F ++V + +
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 49/101 (48%), Gaps = 17/101 (16%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 126
R +F+G + + T E ++ HF+ GT+ + V +R + +G+ +V + E V A++
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 127 LNESELHGRQLK----------------VTVKRTNVPGMKQ 151
++ GR ++ +TVK+ V G+K+
Sbjct: 73 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 113
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 125
+ +FVG + ++ +F+ G + + I TD+ G+ +G+A+V F ++V + +
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 49/101 (48%), Gaps = 17/101 (16%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 126
R +F+G + + T E ++ HF+ GT+ + V +R + +G+ +V + E V A++
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 127 LNESELHGRQLK----------------VTVKRTNVPGMKQ 151
++ GR ++ +TVK+ V G+K+
Sbjct: 74 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 114
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 125
+ +FVG + ++ +F+ G + + I TD+ G+ +G+A+V F ++V + +
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 2/86 (2%)
Query: 56 GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVE 114
GSS ++ + VFVG++ T E+++ F G ++ + D G+ KGY +V
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 115 FLQSEAVQEAL-HLNESELHGRQLKV 139
F + A+ + L GRQ++
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRT 89
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 49/101 (48%), Gaps = 17/101 (16%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 126
R +F+G + + T E ++ HF+ GT+ + V +R + +G+ +V + E V A++
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 127 LNESELHGRQLK----------------VTVKRTNVPGMKQ 151
++ GR ++ +TVK+ V G+K+
Sbjct: 72 ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 112
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL 125
+ +FVG + ++ +F+ G + + I TD+ G+ +G+A+V F ++V + +
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL- 125
S +++VGN+ + T E++ + F G + ++ + DK G+ +VE+ + A+
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 126 HLNESELHGRQLKV 139
++N + L R ++
Sbjct: 78 YINGTRLDDRIIRT 91
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL 125
SR V++G++ Y T E++ + G V + + D + G+ KGYA++EF E+ A+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 126 -HLNESELHGRQLKV 139
+LN +L R LK
Sbjct: 64 RNLNGYQLGSRFLKC 78
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 126
S +FV N+ + T + ++ F CG V I+ + G+ KG V+F E + A
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACR 63
Query: 127 -LNESELHGRQLKVTVKRT 144
+N +L GR++ V + R
Sbjct: 64 MMNGMKLSGREIDVRIDRN 82
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HL 127
V+VG++ Y + ++Q F G + + D + KG+A+VE+ EA Q AL
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 128 NESELHGRQLKV 139
N L GR +KV
Sbjct: 75 NSVXLGGRNIKV 86
Score = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HL 127
++V +V + ++++ F++ G + T+ D G+ KGY ++E+ ++++ Q+A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 128 NESELHGRQLKV 139
N +L G+ L+V
Sbjct: 172 NLFDLGGQYLRV 183
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 2/90 (2%)
Query: 56 GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVE 114
GSS ++ R ++VG + + + F G + + I D + + +G+A+VE
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 115 FLQSEAVQEAL-HLNESELHGRQLKVTVKR 143
F +E A+ ++NESEL GR ++V + +
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL 125
SR V++G++ Y T E++ + G V + + D + G+ KGYA++EF E+ A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 126 -HLNESELHGRQLKV 139
+LN +L R LK
Sbjct: 62 RNLNGYQLGSRFLKC 76
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL 125
SR V++G++ Y T E++ + G V + + D + G+ KGYA++EF E+ A+
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 126 -HLNESELHGRQLKV 139
+LN +L R LK
Sbjct: 63 RNLNGYQLGSRFLKC 77
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 40/71 (56%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLN 128
++FVGN++++ + E++ N + + + G + + YV+F +E +++AL L
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALELT 68
Query: 129 ESELHGRQLKV 139
++ G ++K+
Sbjct: 69 GLKVFGNEIKL 79
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 45/89 (50%), Gaps = 3/89 (3%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQ-SEAVQEALHLN 128
+F+G ++ + ++ F G ++ V + D+ + +G+A++ F ++A A +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 129 ESELHGRQLKVTVKRTNVPGMKQHRPRRP 157
LHG+ +K V++ P + RRP
Sbjct: 70 GKSLHGKAIK--VEQAKKPSFQSGGRRRP 96
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 66 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSEAVQEA 124
D +FVG + + + ++Q F G ++ V + D+ Q +G+ +V F + ++A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 125 -LHLNESELHGRQLKV 139
+ +N + GRQ++V
Sbjct: 71 MMAMNGKSVDGRQIRV 86
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 5/79 (6%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQ-PKGYAYVEFLQSE-AVQEALHL 127
+FV N+ Y+ + E++++ F + G ++ + D + PKG+A+V F+ E AV+ +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 128 NESELHGRQLKV---TVKR 143
+ GR L V T+K+
Sbjct: 71 DGQVFQGRMLHVLPSTIKK 89
>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 = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 62 REEVD-SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSE 119
R+E D + +FVG + P+E ++ F GT+ + DK GQ +G+ +V + ++
Sbjct: 81 RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD 140
Query: 120 AVQEALHLNESELHGRQLKV 139
AV + R++++
Sbjct: 141 AVDRVCQNKFIDFKDRKIEI 160
Score = 34.7 bits (78), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 66 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEA 124
+S +F+G +++ T + ++++F GTV + I D G+ +G+ ++ F + +V E
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 125 L 125
+
Sbjct: 62 V 62
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LN 128
+FV N+ + T + ++ F CG V I+ + G+ KG V+F E + A +N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACRMMN 69
Query: 129 ESELHGRQLKVTVKRT 144
+L GR++ V + R
Sbjct: 70 GMKLSGREIDVRIDRN 85
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF-LQSEAVQEALHLN 128
+ V N+D+ + ++Q+ F GT+ + + D+ G+ G A V F +++A++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 129 ESELHGRQLKVTV 141
L GR + + +
Sbjct: 91 GVPLDGRPMNIQL 103
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 4/81 (4%)
Query: 56 GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 115
GSS R+ R +FVG ++ + ++V++ F++ G + TI G KG A+V++
Sbjct: 4 GSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKY 63
Query: 116 LQSEAVQEALHLNESELHGRQ 136
Q A++ LHG Q
Sbjct: 64 SSHAEAQAAIN----ALHGSQ 80
>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 = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL- 125
R ++VG + + + F G + + I D + + +G+A+VEF +E A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 126 HLNESELHGRQLKVTVKR 143
++NESEL GR ++V + +
Sbjct: 68 NMNESELFGRTIRVNLAK 85
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 1/98 (1%)
Query: 43 GNEMASKQDPAAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRT 101
G+ MAS G + + + V + + + CT EE+ Q F V N +T+
Sbjct: 18 GSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPV 77
Query: 102 DKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 139
D G+ G A+V+F E ++AL ++ + R ++V
Sbjct: 78 DPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEV 115
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLN 128
+FVG + Y T ++++F+ G + + TD+ G+ +GY +V A + A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 129 ESELHGRQLKVTV 141
+ GR+ V +
Sbjct: 80 NPIIDGRKANVNL 92
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 11/86 (12%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLN 128
+FVGNV +CT +E++ F+ G V + D YA+V + + A+ LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 129 ESELHGRQLKVTVKRTNVPGMKQHRP 154
E+ G+++ V + + G K+ P
Sbjct: 65 GKEVKGKRINVEL---STKGQKKSGP 87
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL- 125
R ++VG + + + F G + + I D + + +G+A+VEF +E A+
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 126 HLNESELHGRQLKVTVKR 143
++NESEL GR ++V + +
Sbjct: 66 NMNESELFGRTIRVNLAK 83
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 63 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAV 121
E + +++V N+ + T +++ F G++ + I DK G+P+G A+V + + E
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 122 QEAL 125
QEA+
Sbjct: 69 QEAI 72
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%)
Query: 66 DSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 125
+ R +FVG + T E+V++ F+ GT++ T+ G KG A+V+F Q A+
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
Query: 126 H 126
+
Sbjct: 71 N 71
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF-LQSEAVQEALHLN 128
+ V N+D+ + ++Q+ F GT+ + + D+ G+ G A V F +++A++ N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 129 ESELHGR 135
L GR
Sbjct: 92 GVPLDGR 98
>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 = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPK-GYAYVEFLQSEAVQEAL 125
S +++VGN+ + T E++ + F G + ++ + DK + G+ +VE+ + A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 126 HLNESELHGRQLKVTVKRTNV-PGMKQHR 153
++G +L + RT+ G K+ R
Sbjct: 99 RY----INGTRLDDRIIRTDWDAGFKEGR 123
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF-LQSEAVQEALHLN 128
+ V N+D+ + ++Q+ F GT+ + + D+ G+ G A V F +++A++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 129 ESELHGRQLKVTVKRTNV 146
L GR + + + + +
Sbjct: 151 GVPLDGRPMDIQLVASQI 168
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 25/106 (23%), Positives = 54/106 (50%), Gaps = 15/106 (14%)
Query: 55 GGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYV 113
G S + ++ D+ +F+G + + ++++ F+ G + +T+ D+F G KG A++
Sbjct: 1 GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 114 EFLQSEAVQEALHLNESELHGRQLKVTVKRTNVPGMKQHRPRRPNP 159
+ + E+ +A +S LH ++ +PGM +RP + P
Sbjct: 61 TYCERESALKA----QSALH--------EQKTLPGM--NRPIQVKP 92
>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 = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 63 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAV 121
E + +++V N+ + T +++ F G++ + I DK G+P+G A+V + + E
Sbjct: 96 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 155
Query: 122 QEAL 125
QEA+
Sbjct: 156 QEAI 159
Score = 33.9 bits (76), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 2/87 (2%)
Query: 59 LANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQ 117
L N + ++ V + T E+ F++ G +N I D K G GYA+V+F
Sbjct: 6 LMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTS 65
Query: 118 SEAVQEALH-LNESELHGRQLKVTVKR 143
Q A+ LN + ++LKV+ R
Sbjct: 66 EXDSQRAIKVLNGITVRNKRLKVSYAR 92
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 63 EEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAV 121
E + +++V N+ + T +++ F G++ + I DK G+P+G A+V + + E
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 122 QEAL 125
QEA+
Sbjct: 145 QEAI 148
Score = 33.5 bits (75), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 80 TPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQL 137
T E+ F++ G +N I D K G GYA+V+F Q A+ LN + ++L
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 138 KVTVKR 143
KV+ R
Sbjct: 76 KVSYAR 81
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 28/61 (45%)
Query: 65 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA 124
V+ R +F+G + CT +++ F S G + I G +G A+V F Q A
Sbjct: 105 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTA 164
Query: 125 L 125
+
Sbjct: 165 I 165
>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 = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL- 125
R ++VG + + + F G + + I D + + +G+A+VEF +E A+
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 126 HLNESELHGRQLKVTV 141
++NESEL GR ++V +
Sbjct: 63 NMNESELFGRTIRVNL 78
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 28/61 (45%)
Query: 65 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA 124
V+ R +F+G + CT +++ F S G + I G +G A+V F Q A
Sbjct: 93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTA 152
Query: 125 L 125
+
Sbjct: 153 I 153
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFG--QPKGYAYVEFLQSEAVQEAL-H 126
V +G + + T + + + F + G + + + ++ KGYAYVEF + ++AL H
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 127 LNESELHGRQLKVT 140
++ ++ G+++ T
Sbjct: 67 MDGGQIDGQEITAT 80
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 28/61 (45%)
Query: 65 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA 124
V+ R +F+G + CT +++ F S G + I G +G A+V F Q A
Sbjct: 93 VEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTA 152
Query: 125 L 125
+
Sbjct: 153 I 153
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 35.4 bits (80), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHL 127
+V+VG +D + + + F G V + D+ GQ +GY +VEFL E A+ +
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 128 NES-ELHGRQLKVT 140
+ +L+G+ ++V
Sbjct: 77 MDMIKLYGKPIRVN 90
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.4 bits (80), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 10/89 (11%)
Query: 65 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVN--RVTIRTDKFGQPKGYAYVEFLQSEAVQ 122
+ ++VF+ N+ + E + + Q G + RV + D KG A+ +F+ EA Q
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDT-EHSKGCAFAQFMTQEAAQ 71
Query: 123 EALHLNESE-------LHGRQLKVTVKRT 144
+ L E L GRQLKV + T
Sbjct: 72 KCLAAASLEAEGGGLKLDGRQLKVDLAVT 100
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.0 bits (79), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 65 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEF---LQSEA 120
V+ +FV ++ +E+Q+ F G + + + D + G KGYA VE+ Q+ A
Sbjct: 24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 83
Query: 121 VQEALHLNESELHGRQLKV 139
+EA LN +E+ G+ ++V
Sbjct: 84 AKEA--LNGAEIMGQTIQV 100
>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 = 35.0 bits (79), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 65 VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEF---LQSEA 120
V+ +FV ++ +E+Q+ F G + + + D + G KGYA VE+ Q+ A
Sbjct: 70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129
Query: 121 VQEALHLNESELHGRQLKV 139
+EA LN +E+ G+ ++V
Sbjct: 130 AKEA--LNGAEIMGQTIQV 146
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.7 bits (78), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%)
Query: 56 GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 115
G L R S S+ V N+ + E +++ F G V R + D G+P G VEF
Sbjct: 85 GKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEF 144
Query: 116 LQSEAVQEAL 125
A ++AL
Sbjct: 145 SGKPAARKAL 154
Score = 34.3 bits (77), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQE--ALHL 127
+FVGN+ T EE+++ F+ G V I D KG+ ++ L++ + E + L
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIR-LETRTLAEIAKVEL 78
Query: 128 NESELHGRQLKV 139
+ L G+QL+V
Sbjct: 79 DNMPLRGKQLRV 90
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 34.3 bits (77), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 127
+ F+GN+ Y T E +++ F+ + R+ + KG+ Y EF +++ AL L
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80
Query: 128 NESELHGRQLKVTV 141
NE L R+++V V
Sbjct: 81 NEESLGNRRIRVDV 94
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 34.3 bits (77), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALH 126
S + VGN+ +CT +E++ F+ G V I D YA+V ++E EA+
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIR 62
Query: 127 -LNESELHGRQLKV 139
L+ +E G+++ V
Sbjct: 63 GLDNTEFQGKRMHV 76
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 34.3 bits (77), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 80 TPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQL 137
T E+ F++ G +N I D K G GYA+V+F Q A+ LN + ++L
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 138 KVTVKR 143
KV+ R
Sbjct: 76 KVSYAR 81
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 33.9 bits (76), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF-LQSEAVQEALHLN 128
+ V N+D+ + ++Q+ F GT+ + + D+ G+ G A V F +++A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 129 ESELHGRQLKVTVKRTNV 146
L GR + + + + +
Sbjct: 98 GVPLDGRPMDIQLVASQI 115
>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 = 33.9 bits (76), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEA--LHL 127
+FVGN+ T EE+++ F+ G V I D KG+ ++ L++ + E + L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIR-LETRTLAEIAKVEL 71
Query: 128 NESELHGRQLKV 139
+ L G+QL+V
Sbjct: 72 DNMPLRGKQLRV 83
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 33.9 bits (76), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF-LQSEAVQEALHLN 128
+ V N+D+ + ++Q+ F GT+ + + D+ G+ G A V F +++A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 129 ESELHGRQLKVTVKRTNV 146
L GR + + + + +
Sbjct: 98 GVPLDGRPMDIQLVASQI 115
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 33.9 bits (76), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL- 125
R ++VG + + + F G + + I D + + +G+A+VEF +E A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 126 HLNESELHGRQLKVTV 141
++NESEL GR ++V +
Sbjct: 124 NMNESELFGRTIRVNL 139
>pdb|2LXU|A Chain A, Solution Nmr Structure Of The Eukaryotic Rna Recognition
Motif, Rrm1, From The Heterogeneous Nuclear
Ribonucleoprotein H From Homo Sapiens, Northeast
Structural Genomics Consortium (Nesg) Target Hr8614a
Length = 108
Score = 33.9 bits (76), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 77 YSCTPEEVQQHFQSCGTVN---RVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELH 133
+SC+ +EVQ+ F C N + + G+P G A+VE + V+ AL + +
Sbjct: 17 WSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMG 76
Query: 134 GRQLKVTVKRTNV 146
R ++V K NV
Sbjct: 77 HRYVEV-FKSNNV 88
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.5 bits (75), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 9/91 (9%)
Query: 53 AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYA 111
+ GSS N S+++FV + T E +++ F G+V R I TD+ G KG+
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFG 57
Query: 112 YVEFLQSE---AVQEALHLNESELHGRQLKV 139
+V+F E A +EA+ + E+ G ++ +
Sbjct: 58 FVDFNSEEDAKAAKEAME--DGEIDGNKVTL 86
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALHLN 128
+FVG + + T E+V+ +F+ G V+ + DK + +G+ +V F + V++ ++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 129 ESELHGRQLK 138
E++ + ++
Sbjct: 62 FHEINNKMVE 71
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 120
+R ++VGN+ + T E + F + + +T + + Q K +A++EF +
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 121 VQEALHLNESELHGRQLKV 139
+A+ + G+ LK+
Sbjct: 66 TTQAMAFDGIIFQGQSLKI 84
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 120
+R ++VGN+ + T E + F + + +T + + Q K +A++EF +
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60
Query: 121 VQEALHLNESELHGRQLKV 139
+A+ + G+ LK+
Sbjct: 61 TTQAMAFDGIIFQGQSLKI 79
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCG-TVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 127
+ F+GN+ Y T E +++ F+ + R+ + KG+ Y EF +++ AL L
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76
Query: 128 NESELHGRQLKVTV 141
NE L ++++V V
Sbjct: 77 NEESLGNKRIRVDV 90
>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 = 0.15, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 120
+R ++VGN+ + T E + F + + +T + + Q K +A++EF +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 121 VQEALHLNESELHGRQLKV 139
+A+ + G+ LK+
Sbjct: 64 TTQAMAFDGIIFQGQSLKI 82
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 120
+R ++VGN+ + T E + F + + +T + + Q K +A++EF +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 121 VQEALHLNESELHGRQLKV 139
+A+ + G+ LK+
Sbjct: 64 TTQAMAFDGIIFQGQSLKI 82
>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 = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVT------IRTDKFGQPKGYAYVEFLQSEA 120
+R ++VGN+ + T E + F + + +T + + Q K +A++EF +
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 121 VQEALHLNESELHGRQLKV 139
+A+ + G+ LK+
Sbjct: 66 TTQAMAFDGIIFQGQSLKI 84
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 61 NREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTV-NRVTIRTDKFGQPKGYAYVEFLQSE 119
RE+ R +F+G + + T E ++ +++ G + + V +R + +G+ +V F
Sbjct: 21 KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMA 80
Query: 120 AVQEALHLNESELHGR 135
V A+ + GR
Sbjct: 81 EVDAAMAARPHSIDGR 96
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 79 CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQL 137
TP+ + F G V RV I +K K A V+ Q A+ HLN +LHG+ +
Sbjct: 47 VTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPI 102
Query: 138 KVTVKR 143
++T+ +
Sbjct: 103 RITLSK 108
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 129
++VGN+ ++++ F G + + ++ + G P +A+VEF ++A++ +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP--FAFVEFEDPRDAEDAVYGRD 82
Query: 130 S-ELHGRQLKVTVKRTN 145
+ G +L+V R+
Sbjct: 83 GYDYDGYRLRVEFPRSG 99
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 68 RSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALH 126
R++ V + + +++Q F+ G + V I D+ Q +GY +V+F + Q+A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 127 -LNESELHGRQLKVTV 141
LN + ++LKV +
Sbjct: 103 GLNGFNILNKRLKVAL 118
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 79 CTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQL 137
TP+ + F G V RV I +K K A V+ Q A+ HLN +LHG+ +
Sbjct: 16 VTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPI 71
Query: 138 KVTVKR 143
++T+ +
Sbjct: 72 RITLSK 77
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 46/90 (51%), Gaps = 7/90 (7%)
Query: 56 GSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEF 115
GSS ++ E+ +++VG + + T +++ HF G + +T+ Q + A+++F
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-----QRQQCAFIQF 55
Query: 116 LQSEAVQEALH--LNESELHGRQLKVTVKR 143
+A + A N+ ++GR+L V R
Sbjct: 56 ATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 97 VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 139
+ I + G GY +V+F E V++AL N + GR ++V
Sbjct: 39 IRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEV 81
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 30.4 bits (67), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 25/106 (23%), Positives = 48/106 (45%), Gaps = 5/106 (4%)
Query: 53 AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKF-GQPKGYA 111
+ GSS ++ D+ +FVG + ++++ F+ G + +T+ D+ G KG A
Sbjct: 1 GSSGSSGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCA 60
Query: 112 YVEFLQSEA---VQEALHLNESELHGRQLKVTVKRTNVPGMKQHRP 154
++ + ++ Q ALH + L G + VK G + P
Sbjct: 61 FLTYCARDSALKAQSALH-EQKTLPGMNRPIQVKPAASEGRGESGP 105
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 30.0 bits (66), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 77 YSCTPEEVQQHFQSC---GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 125
+SCT E+V F C N + ++ G+ +G A +E + VQ+AL
Sbjct: 21 WSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 72 VGNVDYSCTPEEVQQHFQSCGT-VNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNES 130
+ N+ +S T +V Q + N V + D GQ G A V+F + +++ L+
Sbjct: 20 ITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRK 79
Query: 131 ELHGRQLKVTV 141
+L+GR+ V V
Sbjct: 80 KLNGREAFVHV 90
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 67 SRSVFVGNVDYSCTPEEVQQHFQSCG-TVNRV-TIRTDKFGQPKGYAYVEFLQSEAVQEA 124
+ S+++G+++ + + F + G TV V IR G P GY +VEF ++
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 125 LH-LNESELHG 134
LH +N L G
Sbjct: 69 LHKINGKPLPG 79
>pdb|2YA1|A Chain A, Product Complex Of A Multi-Modular Glycogen-Degrading
Pneumococcal Virulence Factor Spua
Length = 1014
Score = 29.3 bits (64), Expect = 1.6, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 152 HRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSP 194
HR R MV ++G PF++S YG+ +FR P +P
Sbjct: 792 HRRLRLGNLMVLTAQGT---PFIHSGQEYGRTKQFRNPAYRTP 831
>pdb|2YA2|A Chain A, Catalytic Module Of The Multi-Modular Glycogen-Degrading
Pneumococcal Virulence Factor Spua In Complex With An
Inhibitor
Length = 708
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 152 HRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSP 194
HR R MV ++G PF++S YG+ +FR P +P
Sbjct: 486 HRRLRLGNLMVLTAQGT---PFIHSGQEYGRTKQFRNPAYRTP 525
>pdb|2YA0|A Chain A, Catalytic Module Of The Multi-Modular Glycogen-Degrading
Pneumococcal Virulence Factor Spua
Length = 714
Score = 28.9 bits (63), Expect = 1.7, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 152 HRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSP 194
HR R MV ++G PF++S YG+ +FR P +P
Sbjct: 485 HRRLRLGNLMVLTAQGT---PFIHSGQEYGRTKQFRNPAYRTP 524
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 78 SCTPEEVQQHFQSCGTVNRVT--IRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGR 135
+ T ++++ QS G R +R GQ +G+A+VEF + + N+ L+
Sbjct: 12 AATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNIL 71
Query: 136 QLKVTV 141
KV++
Sbjct: 72 GQKVSM 77
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 9/69 (13%)
Query: 70 VFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNE 129
+FVGN+ T E+ ++ F+ G + V I D +G+ ++ L+S + E + +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIR-LESRTLAE---IAK 75
Query: 130 SELHGRQLK 138
+EL G LK
Sbjct: 76 AELDGTILK 84
>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 = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPK-GYAYVEFLQSEAVQEALH- 126
S++VG++ T + + F G + + + D + GYAYV F Q + AL
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 127 LNESELHGRQLKV 139
+N + G+ +++
Sbjct: 77 MNFDVIKGKPVRI 89
>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 = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 69 SVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPK-GYAYVEFLQSEAVQEALH- 126
S++VG++ T + + F G + + + D + GYAYV F Q + AL
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 127 LNESELHGRQLKV 139
+N + G+ +++
Sbjct: 72 MNFDVIKGKPVRI 84
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 13/84 (15%)
Query: 56 GSSLANREE--VDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAYV 113
GS + +R+E + + +FV E+ + F G + V I G+A+V
Sbjct: 18 GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFV 70
Query: 114 EFLQSEAVQEALHLNESELHGRQL 137
EF ++E+ +A+ E+HG+
Sbjct: 71 EFEEAESAAKAI----EEVHGKSF 90
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 2/93 (2%)
Query: 53 AAGGSSLANREEVDSRSVFVGNVDYSCTPEEVQQHFQSCGTVNRVTIRTDKFGQPKGYAY 112
+ GSS ++ R+++VGN+ T + Q F G + T+ Y +
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCF 59
Query: 113 VEFLQS-EAVQEALHLNESELHGRQLKVTVKRT 144
VEF + +A +N ++ G+++KV T
Sbjct: 60 VEFYEHRDAAAALAAMNGRKILGKEVKVNWATT 92
>pdb|3J27|A Chain A, Cryoem Structure Of Dengue Virus
pdb|3J27|C Chain C, Cryoem Structure Of Dengue Virus
pdb|3J27|E Chain E, Cryoem Structure Of Dengue Virus
pdb|3J2P|A Chain A, Cryoem Structure Of Dengue Virus Capsid Protein
Heterotetramer
pdb|3J2P|C Chain C, Cryoem Structure Of Dengue Virus Capsid Protein
Heterotetramer
Length = 495
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 56/150 (37%), Gaps = 40/150 (26%)
Query: 5 DMDMIETENKQVELDDMKIRLKEMEEEATALRQ--MHAKVGNEMASKQDPAAGGSSLANR 62
D ++IETE KQ LR+ + AK+ N + P G SL
Sbjct: 42 DFELIETEAKQ----------------PATLRKYCIEAKLTNTTTDSRCPTQGEPSL--N 83
Query: 63 EEVDSRSVFVGNVDYSCTPEEVQQHF-QSCGTVNRVTIRT-----------DKFGQPKGY 110
EE D R + C V + + CG + I T K QP+
Sbjct: 84 EEQDKR--------FVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMKGKVVQPENL 135
Query: 111 AYVEFLQSEAVQEALHLNESELHGRQLKVT 140
Y + + +E N++ HG+++K+T
Sbjct: 136 EYTIVITPHSGEEHAVGNDTGKHGKEIKIT 165
>pdb|2HGL|A Chain A, Nmr Structure Of The First Qrrm Domain Of Human Hnrnp F
pdb|2KFY|A Chain A, Nmr Structure Of The First Qrrm Of Hnrnp F In Complex With
Agggau G- Tract Rna
Length = 136
Score = 26.6 bits (57), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 77 YSCTPEEVQQHFQSC----GTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESEL 132
+SC+ E+VQ C G I T + G+ G A+VE + V+ AL + +
Sbjct: 54 WSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESM 112
Query: 133 HGRQLKV 139
R ++V
Sbjct: 113 GHRYIEV 119
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
0.316 0.133 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,705,928
Number of Sequences: 62578
Number of extensions: 207434
Number of successful extensions: 758
Number of sequences better than 100.0: 116
Number of HSP's better than 100.0 without gapping: 57
Number of HSP's successfully gapped in prelim test: 59
Number of HSP's that attempted gapping in prelim test: 673
Number of HSP's gapped (non-prelim): 130
length of query: 196
length of database: 14,973,337
effective HSP length: 94
effective length of query: 102
effective length of database: 9,091,005
effective search space: 927282510
effective search space used: 927282510
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: 49 (23.5 bits)