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= 029897
(185 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 90.5 bits (223), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 43/93 (46%), Positives = 60/93 (64%), Gaps = 12/93 (12%)
Query: 58 SLANREEVDSRSVFVGN-----------QHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFL 105
S ++E+D RSV+VGN HF SCG++NR+TI DKF G PKGYAY+EF
Sbjct: 27 SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA 86
Query: 106 QSEAVQEALHLNESELHGRQLKVTVKRTNVPGM 138
+ +V A+ ++E+ GR +KV KRTN+PG+
Sbjct: 87 ERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGI 119
>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 = 89.7 bits (221), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 45/87 (51%), Positives = 57/87 (65%), Gaps = 12/87 (13%)
Query: 64 EVDSRSVFVGN-----------QHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQ 111
E D+RS++VGN HF CG+VNRVTI DKF G PKG+AY+EF E+V+
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 112 EALHLNESELHGRQLKVTVKRTNVPGM 138
+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 = 89.7 bits (221), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 45/87 (51%), Positives = 57/87 (65%), Gaps = 12/87 (13%)
Query: 64 EVDSRSVFVGN-----------QHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQ 111
E D+RS++VGN HF CG+VNRVTI DKF G PKG+AY+EF E+V+
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 112 EALHLNESELHGRQLKVTVKRTNVPGM 138
+L L+ES GRQ+KV KRTN PG+
Sbjct: 63 TSLALDESLFRGRQIKVIPKRTNRPGI 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 43/80 (53%), Gaps = 13/80 (16%)
Query: 62 REEVDSRSVFVGN-----------QHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAV 110
+EE D R+VFVGN + F G + +VTI D+ G+PK + +V F E+V
Sbjct: 12 QEEAD-RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70
Query: 111 QEALH-LNESELHGRQLKVT 129
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 = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 77 FQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 128
F G+V V I TD+ G KGY +V F VQ+ + ++ HG++LK+
Sbjct: 30 FARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKL 80
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 77 FQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 128
F G+V V I TD+ G KGY +V F VQ+ + ++ HG++LK+
Sbjct: 31 FARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKL 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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 77 FQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 128
F G+V V I TD+ G KGY +V F VQ+ + ++ HG++LK+
Sbjct: 30 FARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKL 80
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 68 RSVFVGN-----------QHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL- 114
RSVFVGN F G V + D+ G+PKGY + E+ E A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 115 HLNESELHGRQLKV 128
+LN E GR L+V
Sbjct: 69 NLNGREFSGRALRV 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 63 EEVDSRSVFVGNQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESE 120
EEVD + V + F G + + I D + + +G+A+VEF +E A+ ++NESE
Sbjct: 22 EEVDDK---VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE 78
Query: 121 LHGRQLKVTVKR 132
L GR ++V + +
Sbjct: 79 LFGRTIRVNLAK 90
>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 = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 63 EEVDSRSVFVGNQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESE 120
EEVD + V + F G + + I D + + +G+A+VEF +E A+ ++NESE
Sbjct: 17 EEVDDK---VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE 73
Query: 121 LHGRQLKVTVKR 132
L GR ++V + +
Sbjct: 74 LFGRTIRVNLAK 85
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 17/76 (22%)
Query: 69 SVFVGNQHFQSC-GTVNRV----TIR---------TDKFGQPKGYAYVEFLQSEAVQEAL 114
+ +VGN F + G ++ + +IR TDKF KG+ YVEF + ++++EAL
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKF---KGFCYVEFDEVDSLKEAL 73
Query: 115 HLNESELHGRQLKVTV 130
+ + L R L+V +
Sbjct: 74 TYDGALLGDRSLRVDI 89
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 14/75 (18%)
Query: 68 RSVFVGN-----------QHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEAL- 114
R+++VGN + F G V V + D+ +PKG+ +VE +Q E+V EA+
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 115 HLNESELHGRQLKVT 129
L+ ++ GR ++VT
Sbjct: 61 KLDNTDFMGRTIRVT 75
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 15/78 (19%)
Query: 68 RSVFVGN-----------QHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHL 116
R ++VGN Q+FQ G + + I DK + YA+VE+ QS AL
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ- 59
Query: 117 NESELHGRQLKVTVKRTN 134
L+G+Q++ + + N
Sbjct: 60 ---TLNGKQIENNIVKIN 74
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 63 EEVDSRSVFVGNQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESE 120
EEVD + V + F G + + I D + + +G+A+VEF +E A+ ++NESE
Sbjct: 15 EEVDDK---VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE 71
Query: 121 LHGRQLKVTVKR 132
L GR ++V + +
Sbjct: 72 LFGRTIRVNLAK 83
>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 = 34.7 bits (78), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 63 EEVDSRSVFVGNQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESE 120
EEVD + V + F G + + I D + + +G+A+VEF +E A+ ++NESE
Sbjct: 12 EEVDDK---VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE 68
Query: 121 LHGRQLKVTV 130
L GR ++V +
Sbjct: 69 LFGRTIRVNL 78
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 34.7 bits (78), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 86 VTIRTDKFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVK 131
+ + ++ G+ KGYA++EF E +EAL+ N+ E+ GR +++ ++
Sbjct: 42 IKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ 88
>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 = 34.3 bits (77), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 77 FQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 132
F+ G + R+ + + + G+P+GYA++E+ + A H + ++ GR++ V V+R
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>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 = 33.9 bits (76), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 77 FQSCGTVNRV-TIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKR 132
F+ G + R+ + + + G+P+GYA++E+ + A H + ++ GR++ V V+R
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 33.5 bits (75), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 63 EEVDSRSVFVGNQHFQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESE 120
EEVD + V + F G + + I D + + +G+A+VEF +E A+ ++NESE
Sbjct: 73 EEVDDK---VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE 129
Query: 121 LHGRQLKVTV 130
L GR ++V +
Sbjct: 130 LFGRTIRVNL 139
>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 = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 81 GTVNRVTIRTDKFGQPKGYAYVEFL-QSEAVQEALHLNESELHGRQLKVTVKRT 133
GTV + + T++ G+PKG AYVE+ +S+A Q + ++ + +KV + +
Sbjct: 42 GTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNS 95
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 77 FQSCGTVNRVTIRTDKFGQPKGYAYVEFLQ-SEAVQEALHLNESELHGRQLKVTVKRTNV 135
F G ++ V + D+ + +G+A++ F ++A A +N LHG+ +K V++
Sbjct: 28 FGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIK--VEQAKK 85
Query: 136 PGMKQHRPRRP 146
P + RRP
Sbjct: 86 PSFQSGGRRRP 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 = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 12/85 (14%)
Query: 53 AAGGSSLA----NREEVDSRSVFVGNQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSE 108
AG S L N E V +S+F+ F G V RV I +K K A V+
Sbjct: 31 GAGNSVLLVSNLNPERVTPQSLFI---LFGVYGDVQRVKILFNK----KENALVQMADGN 83
Query: 109 AVQEAL-HLNESELHGRQLKVTVKR 132
Q A+ HLN +LHG+ +++T+ +
Sbjct: 84 QAQLAMSHLNGHKLHGKPIRITLSK 108
>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 = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 77 FQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVTVKRTN 134
F++ G + T+ D G+ KGY ++E+ ++++ Q+A+ +N +L G+ L+ V +
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLR--VGKAV 203
Query: 135 VPGMKQHRPRRPN 147
P M P P
Sbjct: 204 TPPMPLLTPATPG 216
Score = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 75 QHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 128
Q F G + + + D + KG+A+VE+ EA Q AL +N L GR +KV
Sbjct: 47 QAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
>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 = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 75 QHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNESELHGRQL 126
+F G V T++ D G+ +G+ +V F +SE+V + + E +L+G+ +
Sbjct: 18 DYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVI 70
>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 = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 77 FQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKR 132
F++ G +N I D K G GYA+V+F Q A+ LN + ++LKV+ R
Sbjct: 35 FRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYAR 92
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 77 FQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 114
F G++ + I DK G+P+G A+V + + E QEA+
Sbjct: 121 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 77 FQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKR 132
F++ G +N I D K G GYA+V+F Q A+ LN + ++LKV+ R
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 61 NREEVDSRSVFVGNQHFQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL-HLNES 119
N E V +S+F+ F G V RV I +K K A V+ Q A+ HLN
Sbjct: 12 NPERVTPQSLFI---LFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGH 64
Query: 120 ELHGRQLKVTVKR 132
+LHG+ +++T+ +
Sbjct: 65 KLHGKPIRITLSK 77
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 77 FQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 128
F++ G + T+ D G+ KGY ++E+ ++++ Q+A+ +N +L G+ L+V
Sbjct: 131 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 75 QHFQSCGTVNRVTIRTDKFG-QPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 128
Q F G + + + D + KG+A+VE+ EA Q AL +N L GR +KV
Sbjct: 32 QAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 87
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 77 FQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQ 125
FQ G ++ T+ G KG A+V+F Q A+H LHG Q
Sbjct: 36 FQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH----ALHGSQ 80
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 77 FQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTVKR 132
F++ G +N I D K G GYA+V+F Q A+ LN + ++LKV+ R
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
Score = 27.3 bits (59), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 77 FQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 114
F G++ + I DK G+P+G A+V + + E QEA+
Sbjct: 110 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
>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 = 0.48, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 86 VTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKV 128
+ I + G GY +V+F E V++AL N + GR ++V
Sbjct: 39 IRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEV 81
>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 = 29.6 bits (65), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 77 FQSCGTVNRVTIRTD-KFGQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 128
F++ G + T+ D G+ KGY ++E+ ++++ Q+A+ N +L G+ L+V
Sbjct: 130 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 75 QHFQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 128
Q F G + + D + KG+A+VE+ EA Q AL N L GR +KV
Sbjct: 31 QAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKV 86
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 97 KGYAYVEFLQSEAVQEAL-HLNESELHGRQLKVT 129
KGYAYVEF + ++AL H++ ++ G+++ T
Sbjct: 47 KGYAYVEFENPDEAEKALKHMDGGQIDGQEITAT 80
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 75 QHFQSCGTVNRVTIRTDK-FGQPKGYAYVEFLQSEAVQEALH-LNESELHGRQLKVTV 130
Q F+ G + V I D+ Q +GY +V+F + Q+A+ LN + ++LKV +
Sbjct: 61 QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
>pdb|2YA1|A Chain A, Product Complex Of A Multi-Modular Glycogen-Degrading
Pneumococcal Virulence Factor Spua
Length = 1014
Score = 28.9 bits (63), Expect = 1.5, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 141 HRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSP 183
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 = 1.6, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 141 HRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSP 183
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 = 1.6, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 141 HRPRRPNPFMVYQSRGAIIPPFLYSPYGYGKIPRFRMPMRYSP 183
HR R MV ++G PF++S YG+ +FR P +P
Sbjct: 485 HRRLRLGNLMVLTAQGT---PFIHSGQEYGRTKQFRNPAYRTP 524
>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 = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 94 GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 128
G+ KGYA++EF E+ A+ +LN +L R LK
Sbjct: 42 GRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 77
>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 = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 94 GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 128
G+ KGYA++EF E+ A+ +LN +L R LK
Sbjct: 43 GRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 78
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 94 GQPKGYAYVEFLQSEAVQEAL-HLNESELHGRQLKV 128
G+ KGYA++EF E+ A+ +LN +L R LK
Sbjct: 41 GRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC 76
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 77 FQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEALHLNES-ELHGRQLKVT 129
F G V + D+ GQ +GY +VEFL E A+ + + +L+G+ ++V
Sbjct: 36 FLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN 90
>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 = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 77 FQSCGTVNRVTIRTDKF-GQPKGYAYVEFLQSEAVQEAL 114
F G++ + I DK G+P+G A+V + + E QEA+
Sbjct: 34 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
>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 = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 36/142 (25%), Positives = 53/142 (37%), Gaps = 35/142 (24%)
Query: 5 DMDMIETENKQVELDDMKIRLKEMEEEATALRQ--MHAKVGNEMASKQDPAAGGSSLANR 62
D ++IETE KQ LR+ + AK+ N + P G SL
Sbjct: 42 DFELIETEAKQ----------------PATLRKYCIEAKLTNTTTDSRCPTQGEPSL--N 83
Query: 63 EEVDSRSV----FVGNQHFQSCGTVNRVTIRT-----------DKFGQPKGYAYVEFLQS 107
EE D R V V CG + I T K QP+ Y +
Sbjct: 84 EEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMKGKVVQPENLEYTIVITP 143
Query: 108 EAVQEALHLNESELHGRQLKVT 129
+ +E N++ HG+++K+T
Sbjct: 144 HSGEEHAVGNDTGKHGKEIKIT 165
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 27.7 bits (60), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 18/38 (47%)
Query: 77 FQSCGTVNRVTIRTDKFGQPKGYAYVEFLQSEAVQEAL 114
F G V R + D G+P G VEF A ++AL
Sbjct: 117 FSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
>pdb|2X2H|A Chain A, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase
pdb|2X2H|B Chain B, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase
pdb|2X2H|C Chain C, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase
pdb|2X2H|D Chain D, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase
pdb|2X2I|A Chain A, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase With Acarbose
pdb|2X2I|B Chain B, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase With Acarbose
pdb|2X2I|C Chain C, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase With Acarbose
pdb|2X2I|D Chain D, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase With Acarbose
pdb|2X2J|A Chain A, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase With Deoxynojirimycin
pdb|2X2J|B Chain B, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase With Deoxynojirimycin
pdb|2X2J|C Chain C, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase With Deoxynojirimycin
pdb|2X2J|D Chain D, Crystal Structure Of The Gracilariopsis Lemaneiformis
Alpha- 1,4-Glucan Lyase With Deoxynojirimycin
Length = 1027
Score = 26.9 bits (58), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 10 ETENKQVELDDMKIRLKEMEEEATALRQMHAKVGNEMASKQDPAAGGSSLAN--REEVDS 67
+T + QV + DM+ E T R +HA E K+ +L R + S
Sbjct: 579 KTYHPQVLVTDMRYENHGREPMVTQ-RNIHAYTLCESTRKEGIVENADTLTKFRRSYIIS 637
Query: 68 RSVFVGNQHF 77
R ++GNQHF
Sbjct: 638 RGGYIGNQHF 647
>pdb|3C5X|A Chain A, Crystal Structure Of The Precursor Membrane Protein-
Envelope Protein Heterodimer From The Dengue 2 Virus At
Low Ph
pdb|3C6E|A Chain A, Crystal Structure Of The Precursor Membrane Protein-
Envelope Protein Heterodimer From The Dengue 2 Virus At
Neutral Ph
Length = 402
Score = 26.6 bits (57), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 35/142 (24%), Positives = 53/142 (37%), Gaps = 35/142 (24%)
Query: 5 DMDMIETENKQVELDDMKIRLKEMEEEATALRQ--MHAKVGNEMASKQDPAAGGSSLANR 62
D ++I+TE KQ LR+ + AK+ N + P G SL
Sbjct: 50 DFELIKTEAKQ----------------PATLRKYCIEAKLTNTTTESRCPTQGEPSL--N 91
Query: 63 EEVDSRSV----FVGNQHFQSCGTVNRVTIRT-----------DKFGQPKGYAYVEFLQS 107
EE D R V V CG + I T K QP+ Y +
Sbjct: 92 EEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFRCKKNMEGKVVQPENLEYTIVITP 151
Query: 108 EAVQEALHLNESELHGRQLKVT 129
+ +E N++ HG+++K+T
Sbjct: 152 HSGEEHAVGNDTGKHGKEIKIT 173
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 26.6 bits (57), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 84 NRVTIRTDKFGQPKGYAYVEFLQSEAVQEALHLNESELHGRQLKVTV 130
N V + D GQ G A V+F + +++ L+ +L+GR+ V V
Sbjct: 44 NAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV 90
>pdb|3C6D|A Chain A, The Pseudo-Atomic Structure Of Dengue Immature Virus
pdb|3C6D|B Chain B, The Pseudo-Atomic Structure Of Dengue Immature Virus
pdb|3C6D|C Chain C, The Pseudo-Atomic Structure Of Dengue Immature Virus
pdb|3C6R|A Chain A, Low Ph Immature Dengue Virus
pdb|3C6R|B Chain B, Low Ph Immature Dengue Virus
pdb|3C6R|C Chain C, Low Ph Immature Dengue Virus
pdb|3IXY|A Chain A, The Pseudo-Atomic Structure Of Dengue Immature Virus In
Complex With Fab Fragments Of The Anti-Fusion Loop
Antibody E53
pdb|3IXY|B Chain B, The Pseudo-Atomic Structure Of Dengue Immature Virus In
Complex With Fab Fragments Of The Anti-Fusion Loop
Antibody E53
pdb|3IXY|C Chain C, The Pseudo-Atomic Structure Of Dengue Immature Virus In
Complex With Fab Fragments Of The Anti-Fusion Loop
Antibody E53
pdb|3IYA|A Chain A, Association Of The Pr Peptides With Dengue Virus Blocks
Memb Fusion At Acidic Ph
pdb|3IYA|B Chain B, Association Of The Pr Peptides With Dengue Virus Blocks
Memb Fusion At Acidic Ph
pdb|3IYA|C Chain C, Association Of The Pr Peptides With Dengue Virus Blocks
Memb Fusion At Acidic Ph
Length = 395
Score = 26.6 bits (57), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 35/142 (24%), Positives = 53/142 (37%), Gaps = 35/142 (24%)
Query: 5 DMDMIETENKQVELDDMKIRLKEMEEEATALRQ--MHAKVGNEMASKQDPAAGGSSLANR 62
D ++I+TE KQ LR+ + AK+ N + P G SL
Sbjct: 42 DFELIKTEAKQ----------------PATLRKYCIEAKLTNTTTESRCPTQGEPSL--N 83
Query: 63 EEVDSRSV----FVGNQHFQSCGTVNRVTIRT-----------DKFGQPKGYAYVEFLQS 107
EE D R V V CG + I T K QP+ Y +
Sbjct: 84 EEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFRCKKNMEGKVVQPENLEYTVVITP 143
Query: 108 EAVQEALHLNESELHGRQLKVT 129
+ +E N++ HG+++K+T
Sbjct: 144 HSGEEHAVGNDTGKHGKEVKIT 165
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.133 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,294,723
Number of Sequences: 62578
Number of extensions: 190438
Number of successful extensions: 627
Number of sequences better than 100.0: 56
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 595
Number of HSP's gapped (non-prelim): 62
length of query: 185
length of database: 14,973,337
effective HSP length: 93
effective length of query: 92
effective length of database: 9,153,583
effective search space: 842129636
effective search space used: 842129636
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)