RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17775
(211 letters)
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 86.1 bits (213), Expect = 3e-21
Identities = 34/103 (33%), Positives = 48/103 (46%), Gaps = 4/103 (3%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQVFLSDVSHPYELPDGSESFKDF 163
+VQM D A+ AM +L+ L +GK + + SK +V P E + KD+
Sbjct: 42 ENALVQMADGNQAQLAMSHLNGHKL-HGKPIRITLSKH---QNVQLPREGQEDQGLTKDY 97
Query: 164 TGSRKNRFMNPKMAMKNRIQPPSQLLHFFNAPPDITEEQLTDI 206
S +RF P I PPS LH N PP ++EE L +
Sbjct: 98 GNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVL 140
Score = 32.2 bits (73), Expect = 0.076
Identities = 11/43 (25%), Positives = 18/43 (41%)
Query: 99 PSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
++QMG A +A+ +L L L V++SK
Sbjct: 154 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 79.4 bits (195), Expect = 1e-18
Identities = 46/103 (44%), Positives = 64/103 (62%), Gaps = 2/103 (1%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQVFLSDVSHPYELPDGSESFKDF 163
G MV+M D + +RA+ +L+ + +++ V SKQ + Y L DGS S+KDF
Sbjct: 43 GAAMVEMADGYAVDRAITHLNNNFMFG-QKMNVCVSKQPAIMP-GQSYGLEDGSCSYKDF 100
Query: 164 TGSRKNRFMNPKMAMKNRIQPPSQLLHFFNAPPDITEEQLTDI 206
+ SR NRF P+ A KNRIQ PS +LHFFNAP ++TEE +I
Sbjct: 101 SESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEI 143
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 77.7 bits (191), Expect = 7e-18
Identities = 34/103 (33%), Positives = 48/103 (46%), Gaps = 4/103 (3%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQVFLSDVSHPYELPDGSESFKDF 163
+VQM D A+ AM +L+ L +GK + + SK +V P E + KD+
Sbjct: 73 ENALVQMADGNQAQLAMSHLNGHKL-HGKPIRITLSKH---QNVQLPREGQEDQGLTKDY 128
Query: 164 TGSRKNRFMNPKMAMKNRIQPPSQLLHFFNAPPDITEEQLTDI 206
S +RF P I PPS LH N PP ++EE L +
Sbjct: 129 GNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVL 171
Score = 31.1 bits (70), Expect = 0.20
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
++QMG A +A+ +L L L V++SK
Sbjct: 190 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 227
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 43.5 bits (102), Expect = 4e-06
Identities = 16/25 (64%), Positives = 22/25 (88%)
Query: 2 SAPTKLNVYKNDSESWDYTQPTLGR 26
+ PT+LNV +ND++SWDYT+P LGR
Sbjct: 99 ARPTRLNVIRNDNDSWDYTKPYLGR 123
Score = 27.7 bits (61), Expect = 1.7
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 8/66 (12%)
Query: 106 CMVQMGDTLSAERAMGNLSKTLLCNGK-RLAVAYSKQVFLSDVSHPYELPDGSESFKDFT 164
MV+ L A++A L+ + G L + Y++ L+ + D+T
Sbjct: 65 AMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLN-------VIRNDNDSWDYT 117
Query: 165 GSRKNR 170
R
Sbjct: 118 KPYLGR 123
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 40.9 bits (95), Expect = 7e-05
Identities = 15/52 (28%), Positives = 20/52 (38%), Gaps = 9/52 (17%)
Query: 2 SAPTKLNVYKNDSESWDYTQPTLGRTKDGPPSRPGPLLPEPPRRLPTPSGPP 53
S T LNV N+ +S DYT+P L G P + + G
Sbjct: 121 SKLTSLNVKYNNDKSRDYTRPDLP---------SGDSQPSLDQTMAAAFGLS 163
Score = 29.7 bits (66), Expect = 0.43
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 89 IGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNG-KRLAVAYSKQVFLS 145
G + + ++Q D +SA+ A +L + N L + +SK L+
Sbjct: 70 FGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN 127
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 36.9 bits (85), Expect = 0.001
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 2 SAPTKLNVYKNDSESWDYTQPTLGRT 27
S T LNV N+ +S DYT+P L
Sbjct: 103 SKLTSLNVKYNNDKSRDYTRPDLPSG 128
Score = 30.0 bits (67), Expect = 0.24
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 89 IGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNG-KRLAVAYSKQVFLS 145
G + + ++Q D +SA+ A +L + N L + +SK L+
Sbjct: 52 FGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN 109
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 34.9 bits (80), Expect = 0.004
Identities = 10/48 (20%), Positives = 17/48 (35%)
Query: 159 SFKDFTGSRKNRFMNPKMAMKNRIQPPSQLLHFFNAPPDITEEQLTDI 206
S S M PS+++H P D+TE ++ +
Sbjct: 4 SHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISL 51
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 35.2 bits (80), Expect = 0.010
Identities = 17/147 (11%), Positives = 31/147 (21%), Gaps = 23/147 (15%)
Query: 18 DYTQPTLGRTKDGPPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYPDDDYYGAPPAFEFE 77
P G R +P P +P P P G P
Sbjct: 136 AVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQM 195
Query: 78 RSYNSPVLDKFIGKPRGMSGPPS-----------------------GPEGCCMVQMGDTL 114
+ + P G V+ + +
Sbjct: 196 PPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEV 255
Query: 115 SAERAMGNLSKTLLCNGKRLAVAYSKQ 141
A A L + + ++++K+
Sbjct: 256 QAGAARDALQGFKITQNNAMKISFAKK 282
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 32.1 bits (73), Expect = 0.031
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 172 MNPKMAMKNR-IQPPSQLLHFFNAPPDITEEQLTDI 206
M + PS+++H P D+TE ++ +
Sbjct: 1 MRGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISL 36
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 32.1 bits (73), Expect = 0.034
Identities = 4/34 (11%), Positives = 11/34 (32%)
Query: 173 NPKMAMKNRIQPPSQLLHFFNAPPDITEEQLTDI 206
+ + + S ++H + E L +
Sbjct: 2 SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEA 35
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 32.0 bits (73), Expect = 0.034
Identities = 5/23 (21%), Positives = 9/23 (39%)
Query: 184 PPSQLLHFFNAPPDITEEQLTDI 206
P S ++H + E L +
Sbjct: 19 PASPVVHIRGLIDGVVEADLVEA 41
Score = 28.2 bits (63), Expect = 0.76
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 1/38 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLS-KTLLCNGKRLAVAYSK 140
+V+ D L A A+ + + G V YS
Sbjct: 58 RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 31.7 bits (72), Expect = 0.044
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 179 KNRIQPPSQLLHFFNAPPDITEEQLTDI 206
PS++LH P ++TE ++ +
Sbjct: 8 DKMDGAPSRVLHIRKLPGEVTETEVIAL 35
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 31.4 bits (72), Expect = 0.045
Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
G V + SA A+ ++ K + + Y+K
Sbjct: 52 GQAFVIFKEVSSATNALRSMQGFPFY-DKPMRIQYAKT 88
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 31.8 bits (72), Expect = 0.053
Identities = 6/38 (15%), Positives = 12/38 (31%), Gaps = 1/38 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
G + SA+ + G L + +S+
Sbjct: 73 GKAYIVFATQESAQAFVEAFQGYPFQ-GNPLVITFSET 109
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 30.7 bits (70), Expect = 0.080
Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 10/57 (17%)
Query: 84 VLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
L + G V D A RA+ LS + +GK + V YS
Sbjct: 35 PLAGQVLLKSG----------YAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV 81
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 30.6 bits (69), Expect = 0.11
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 101 GPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
GP + D+ +A++A+ L L L VA ++Q
Sbjct: 54 GPRRRAFLHYPDSAAAQQAVSCLQGLRLG-TDTLRVALARQ 93
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 30.4 bits (69), Expect = 0.13
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 13/61 (21%)
Query: 84 VLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKT---LLCNGKRLAVAYSK 140
+ DK + RG VQ+ + A + + L L +GK + V ++K
Sbjct: 44 IKDKQTQQNRGF----------AFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK 93
Query: 141 Q 141
Sbjct: 94 S 94
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 30.4 bits (69), Expect = 0.16
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
G V D A+ A+ +LS + + + L V Y
Sbjct: 48 GTAYVVYEDIFDAKNAVDHLSGFNV-SNRYLVVLYYNA 84
Score = 25.4 bits (56), Expect = 7.8
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 181 RIQP-PSQLLHFFNAPPDITEEQLTDI 206
R+ P +++L+ N P IT E++ DI
Sbjct: 2 RLPPEVNRILYIRNLPYKITAEEMYDI 28
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 28.4 bits (64), Expect = 0.46
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
C +Q +AE A L+ NG+RL V + +
Sbjct: 49 QCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 28.8 bits (65), Expect = 0.50
Identities = 8/37 (21%), Positives = 14/37 (37%), Gaps = 1/37 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
GCC ++ A + L+ G+ L + K
Sbjct: 64 GCCFIKYDTHEQAAVCIVALANFPF-QGRNLRTGWGK 99
>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
Length = 168
Score = 28.7 bits (64), Expect = 0.94
Identities = 13/58 (22%), Positives = 19/58 (32%), Gaps = 2/58 (3%)
Query: 1 MSAPTKLNVYKNDSESWDYTQPTLGRTKDGPPSRPGPLLPEPPRRLPTPSGPPSMPNY 58
+S S + + G + PPS P L + P P PP + Y
Sbjct: 10 LSNYGPYVKAIALDFSGSFFEGGFGGLDEDPPSTPPAGLAVEEK--PEPQCPPGLRQY 65
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 27.7 bits (62), Expect = 1.4
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 102 PEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
+G VQ + A A+ + +L G+ L + +
Sbjct: 61 HKGYAFVQYSNERHARAAVLGENGRVLA-GQTLDINMAG 98
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 27.3 bits (61), Expect = 1.8
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 102 PEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
G V+ + SA +A+ + + L V YSK
Sbjct: 64 LNGFAFVEFEEAESAAKAIEEVHGKSFA-NQPLEVVYSK 101
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 26.9 bits (60), Expect = 1.9
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
V + A AM L+ +L +G + V +K
Sbjct: 52 DYAFVHFSNREDAVEAMKALNGKVL-DGSPIEVTLAK 87
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 26.9 bits (60), Expect = 1.9
Identities = 8/33 (24%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 108 VQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
+Q + S A+ S+ + GK+L + S
Sbjct: 62 IQFDNPQSVRDAIEXESQEMNF-GKKLILEVSS 93
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 27.3 bits (61), Expect = 1.9
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
G V+ SA A+ +++ T + G + + K
Sbjct: 62 GYSFVRFSTHESAAHAIVSVNGTTI-EGHVVKCYWGK 97
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 26.8 bits (60), Expect = 2.0
Identities = 8/33 (24%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 108 VQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
+Q + S A+ S+ + GK+L + S
Sbjct: 50 IQFDNPQSVRDAIECESQEMNF-GKKLILEVSS 81
>2z3y_A Lysine-specific histone demethylase 1; chromatin, nucleosome,
transcription, LSD1, alternative splicing, chromatin
regulator, coiled coil; HET: F2N; 2.25A {Homo sapiens}
SCOP: a.4.1.18 c.3.1.2 d.16.1.5 PDB: 2ejr_A* 2z5u_A*
3abt_A* 3abu_A* 2y48_A* 2v1d_A* 2h94_A* 2iw5_A* 2uxn_A*
2uxx_A* 2hko_A* 2dw4_A* 2x0l_A* 2l3d_A
Length = 662
Score = 28.3 bits (62), Expect = 2.1
Identities = 13/81 (16%), Positives = 21/81 (25%), Gaps = 12/81 (14%)
Query: 45 RLPTPSGPPSMPNYRGGYPDDDYYGAPPAFEFERSYNSPVLDKFIGKPRGMSGPPSGPEG 104
PS+ G+ F F Y +P+L + G
Sbjct: 494 CFDRVFWDPSV--NLFGHVGSTTASRGELFLFWNLYKAPILLALVA----------GEAA 541
Query: 105 CCMVQMGDTLSAERAMGNLSK 125
M + D + R + L
Sbjct: 542 GIMENISDDVIVGRCLAILKG 562
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 27.5 bits (62), Expect = 2.2
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
G V + ++RA+ L+ + KRL V+Y++
Sbjct: 46 GYAFVDFTSEMDSQRAIKVLNGITV-RNKRLKVSYARP 82
>2xij_A Methylmalonyl-COA mutase, mitochondrial; isomerase, organic
aciduria, vitamin B12; HET: B12 5AD BTB; 1.95A {Homo
sapiens} PDB: 2xiq_A* 3bic_A
Length = 762
Score = 28.1 bits (63), Expect = 2.2
Identities = 20/82 (24%), Positives = 24/82 (29%), Gaps = 6/82 (7%)
Query: 3 APTKLNVYKNDSESWDYTQPTLGRTKDGPP----SRPGPLLPEPPRRLP--TPSGPPSMP 56
+P L K S S Q L + + P L + P L TP G P
Sbjct: 2 SPHYLRQVKESSGSRLIQQRLLHQQQPLHPEWAALAKKQLKGKNPEDLIWHTPEGISIKP 61
Query: 57 NYRGGYPDDDYYGAPPAFEFER 78
Y D P F R
Sbjct: 62 LYSKRDTMDLPEELPGVKPFTR 83
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 26.9 bits (60), Expect = 2.3
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
C V SA++A+ L+ T + +L V ++
Sbjct: 50 NCAFVTYEKMESADQAVAELNGTQV-ESVQLKVNIAR 85
>3dbg_A Putative cytochrome P450; cytochrome P450 oxidoreductase,
CYP170A1, molecular mechanism, heme, iron,
metal-binding, monooxygenase; HET: HEM; 2.60A
{Streptomyces coelicolor A3} PDB: 3el3_A*
Length = 467
Score = 28.0 bits (63), Expect = 2.4
Identities = 6/25 (24%), Positives = 7/25 (28%)
Query: 32 PSRPGPLLPEPPRRLPTPSGPPSMP 56
P P P P P +P
Sbjct: 8 PETRAPAAPGAPELREPPVAGGGVP 32
>2ast_A S-phase kinase-associated protein 1A; SCF-substrate complex, LRR,
cell cycle, protein turnover COM ligase-ligase inhibitor
complex; HET: TPO; 2.30A {Homo sapiens} PDB: 2ass_A*
2e31_B 2e32_B 3l2o_A 1p22_B* 2ovr_A* 2ovp_A 1fqv_B*
2ovq_A*
Length = 159
Score = 27.1 bits (59), Expect = 2.7
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 175 KMAMKNRIQPPSQLLHFFNAPPDITEEQLTDI 206
+A + + P ++ FN D TEE+ +
Sbjct: 121 TVANMIKGKTPEEIRKTFNIKNDFTEEEEAQV 152
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 26.7 bits (59), Expect = 3.0
Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 95 MSGPPSGPEGCCMVQMGDTLSAERAMGNLSK-TLLCNGKRLAVAYSK 140
+ G V+ +A A L + G ++AV +++
Sbjct: 44 SAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAE 90
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 26.6 bits (59), Expect = 3.2
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 183 QPPSQLLHFFNAPPDITEEQLTDI 206
Q P + + F ++ E L D+
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDM 26
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 26.6 bits (59), Expect = 3.2
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
C V SA++A+ L+ T + +L V ++
Sbjct: 74 NCAFVTYEKMESADQAVAELNGTQV-ESVQLKVNIAR 109
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, P transferase; HET:
GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A*
2vg4_A
Length = 284
Score = 27.2 bits (61), Expect = 3.8
Identities = 11/51 (21%), Positives = 15/51 (29%)
Query: 37 PLLPEPPRRLPTPSGPPSMPNYRGGYPDDDYYGAPPAFEFERSYNSPVLDK 87
P LP P PT + P P Y G + +P +
Sbjct: 2 PQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRIPA 52
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 27.6 bits (61), Expect = 3.8
Identities = 13/66 (19%), Positives = 16/66 (24%), Gaps = 4/66 (6%)
Query: 11 KNDSESWDYTQPTLGRTKDGPPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYPDDDY--- 67
+D+ + P P P G P GYP Y
Sbjct: 359 SSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQ 418
Query: 68 -YGAPP 72
Y PP
Sbjct: 419 GYPPPP 424
Score = 26.0 bits (57), Expect = 9.9
Identities = 14/43 (32%), Positives = 14/43 (32%), Gaps = 3/43 (6%)
Query: 31 PPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYPDDDYYGAPPA 73
PP P P P P P G P GAPPA
Sbjct: 396 PPQGYPPQGYPPQGYPPQGYPPQGYPPPPQGAPP---QGAPPA 435
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 26.1 bits (58), Expect = 3.9
Identities = 8/37 (21%), Positives = 15/37 (40%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
G V A++A L + G+RL + ++
Sbjct: 59 GFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWAD 95
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 26.3 bits (58), Expect = 4.0
Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 98 PPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCN 130
P G +V+ + L A +A +L+ + +
Sbjct: 43 PEGG--ITAIVEFLEPLEARKAFRHLAYSKFHH 73
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 26.8 bits (60), Expect = 4.2
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
G V D AE+A+ L+ L K + V+Y++
Sbjct: 45 GYGFVNYIDPKDAEKAINTLNGLRL-QTKTIKVSYARP 81
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 26.1 bits (58), Expect = 4.3
Identities = 7/38 (18%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
C V+ + A A+ ++ + GK + V ++
Sbjct: 56 PYCFVEFYEHRDAAAALAAMNGRKI-LGKEVKVNWATT 92
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 26.9 bits (60), Expect = 4.4
Identities = 17/124 (13%), Positives = 33/124 (26%), Gaps = 30/124 (24%)
Query: 83 PVLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQV 142
PVL I + + ++ +AM + G+ L +
Sbjct: 41 PVLAVQINQDKN----------FAFLEFRSVDETTQAMA-FDGIIF-QGQSLKIRRP--- 85
Query: 143 FLSDVSHPYELPDGSESFKDFTGSRKNRFMNPKMAMKNRIQPPSQLLHFFNAPPDITEEQ 202
H Y+ G + P A K L P + ++Q
Sbjct: 86 ------HDYQPLPGMSENPSVYVPGVVSTVVPDSAHK---------LFIGGLPNYLNDDQ 130
Query: 203 LTDI 206
+ ++
Sbjct: 131 VKEL 134
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 26.7 bits (59), Expect = 4.4
Identities = 12/57 (21%), Positives = 19/57 (33%), Gaps = 11/57 (19%)
Query: 84 VLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
LDK G C V+ AE AM ++ T L + + + +
Sbjct: 72 GLDKMKKTACGF----------CFVEYYSRADAENAMRYINGTRL-DDRIIRTDWDA 117
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 25.8 bits (57), Expect = 5.1
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 12/57 (21%)
Query: 86 DKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNL--SKTLLCNGKRLAVAYSK 140
D+F G +G C + + SA +A L KTL + + V +
Sbjct: 48 DRFTGMHKG----------CAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94
>3v7d_A Suppressor of kinetochore protein 1; WD 40 domain, phospho-peptide
complex, E3 ubiquitin ligase, cell cycle, phospho
binding protein, phosphorylation; HET: SEP; 2.31A
{Saccharomyces cerevisiae} PDB: 1nex_A* 3mks_A*
Length = 169
Score = 26.3 bits (57), Expect = 5.3
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 175 KMAMKNRIQPPSQLLHFFNAPPDITEEQ 202
+A R + P ++ FN D T E+
Sbjct: 128 VVAEMIRGRSPEEIRRTFNIVNDFTPEE 155
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 25.7 bits (57), Expect = 5.4
Identities = 10/57 (17%), Positives = 19/57 (33%), Gaps = 11/57 (19%)
Query: 84 VLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
LD+ G +G +V+ A A L+ + G+ + V +
Sbjct: 59 NLDRRTGFSKGY----------ALVEYETHKQALAAKEALNGAEI-MGQTIQVDWCF 104
>3odu_A C-X-C chemokine receptor type 4, lysozyme chimera; structural
genomics, PSI-2, protein structure initiative; HET: ITD
OLC OLA; 2.50A {Homo sapiens} PDB: 3oe8_A* 3oe6_A*
3oe0_A* 3oe9_A* 2k03_B* 2k04_B 2k05_B*
Length = 502
Score = 26.8 bits (59), Expect = 5.7
Identities = 9/21 (42%), Positives = 9/21 (42%)
Query: 62 YPDDDYYGAPPAFEFERSYNS 82
Y DDD GAP S N
Sbjct: 2 YKDDDDAGAPEGISIYTSDNY 22
>1ti6_A Pyrogallol hydroxytransferase large subunit; molybdenum binding
enzyme, MGD-cofactors, DMSO-reductase family,
4Fe-4S-cluster; HET: MGD BTT; 2.00A {Pelobacter
acidigallici} SCOP: b.52.2.2 c.81.1.1 PDB: 1ti2_A*
1ti4_A* 1vld_M* 1vle_M* 1vlf_M*
Length = 875
Score = 26.5 bits (58), Expect = 7.4
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 7/71 (9%)
Query: 25 GRTKDGPPSRPGPLLPEPPRRLPTPSG-----PPSMPNYRGGYPDDDYYGAPPAF--EFE 77
GR KD P P + L T +G S+ N+ D++ + + +E
Sbjct: 660 GREKDTPDWGPRLNNQVCRKGLQTTTGKVEFIATSLKNFEEQGYIDEHRPSMHTYVPAWE 719
Query: 78 RSYNSPVLDKF 88
+SP+ K+
Sbjct: 720 SQKHSPLAVKY 730
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 24.8 bits (55), Expect = 8.8
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVA 137
GC +V+ AERA ++ L +G+ + V
Sbjct: 49 GCGVVKFESPEVAERACRMMNGMKL-SGREIDVR 81
>3sqr_A Laccase; multicopper oxidase, glycosylation, oxidoreductase; HET:
NAG BMA MAN; 1.67A {Botrytis aclada}
Length = 580
Score = 26.3 bits (58), Expect = 9.9
Identities = 7/44 (15%), Positives = 12/44 (27%)
Query: 30 GPPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYPDDDYYGAPPA 73
P+ L P + S + D ++Y P
Sbjct: 21 AIPAVRSTLTPRQNTTASCANSATSRSCWGEYSIDTNWYDVTPT 64
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.314 0.135 0.419
Gapped
Lambda K H
0.267 0.0549 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,392,193
Number of extensions: 205544
Number of successful extensions: 847
Number of sequences better than 10.0: 1
Number of HSP's gapped: 771
Number of HSP's successfully gapped: 132
Length of query: 211
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 122
Effective length of database: 4,216,824
Effective search space: 514452528
Effective search space used: 514452528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.4 bits)