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= 013267
(446 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 131 bits (330), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 76/201 (37%), Positives = 118/201 (58%), Gaps = 9/201 (4%)
Query: 245 PGITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQA 304
PG+ G + +LVSNLN +R+ LF LF +YG++ R+K+L NK ++ALVQM DG QA
Sbjct: 27 PGLAGAGN-SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQA 85
Query: 305 ELAVHFLKGALLFGKRLEVNFSKHPNIT---QGAD----THEYMNSNLNRFNRNAAKNYR 357
+LA+ L G L GK + + SKH N+ +G + T +Y NS L+RF + +KN++
Sbjct: 86 QLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQ 145
Query: 358 YCCSPTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQALVLFETEEQATEA 417
P+ +HLS +P V+EE++ +G +V F +K AL+ + E+A +A
Sbjct: 146 NIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQA 205
Query: 418 LVCKHASSLG-GSIIRISFSQ 437
L+ H LG +R+SFS+
Sbjct: 206 LIDLHNHDLGENHHLRVSFSK 226
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 4 PSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQ--ALLQMQDVPSAINAL 58
PS +H+ N+ +SE DL LF G + K K++ AL+QM V A+ AL
Sbjct: 150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 206
Score = 28.1 bits (61), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 372 PQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQALVLFETEEQATEALVCKHASSLGGSII 431
P+ VT + + +G + K+ N K+ ALV QA A+ + L G I
Sbjct: 44 PERVTPQSLFILFGVYGDVQRVKIL-FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPI 102
Query: 432 RISFSQLQSIR 442
RI+ S+ Q+++
Sbjct: 103 RITLSKHQNVQ 113
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 127 bits (319), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 73/192 (38%), Positives = 113/192 (58%), Gaps = 8/192 (4%)
Query: 254 CTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFLKG 313
+LVSNLN +R+ LF LF +YG++ R+K+L NK ++ALVQM DG QA+LA+ L G
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 63
Query: 314 ALLFGKRLEVNFSKHPNIT---QGAD----THEYMNSNLNRFNRNAAKNYRYCCSPTKMI 366
L GK + + SKH N+ +G + T +Y NS L+RF + +KN++ P+ +
Sbjct: 64 HKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATL 123
Query: 367 HLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQALVLFETEEQATEALVCKHASSL 426
HLS +P V+EE++ +G +V F +K AL+ + E+A +AL+ H L
Sbjct: 124 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 183
Query: 427 G-GSIIRISFSQ 437
G +R+SFS+
Sbjct: 184 GENHHLRVSFSK 195
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 4 PSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQ--ALLQMQDVPSAINAL 58
PS +H+ N+ +SE DL LF G + K K++ AL+QM V A+ AL
Sbjct: 119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 175
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 112 bits (281), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 53/106 (50%), Positives = 73/106 (68%), Gaps = 2/106 (1%)
Query: 94 GDEPNRILLVTIHHMLYPITVEVLHQVFSPHGFVEKIVTFQKSAGFQALIQYQLRPSAVV 153
G P +L + + ++ YP+T++VLHQ+FS G V KI+TF K+ FQAL+QY SA
Sbjct: 42 GQSP--VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQH 99
Query: 154 ARSSLQGRNIYDGCCQLDIQFSNLDELQVNYNNERSRDFTNPNLPA 199
A+ SL G+NIY+ CC L I FS L L V YNN++SRD+T P+LP+
Sbjct: 100 AKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPS 145
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 16/100 (16%)
Query: 3 EPSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKN--QALLQMQDVPSAINALQF 60
P I V N+ + ++ + L Q+F FG + K++ N QALLQ D SA +A
Sbjct: 44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHA--- 100
Query: 61 YTNVQPTIRGRNVY-------VQFSSHQELTTMEQNAQGR 93
+ ++ G+N+Y + FS L N + R
Sbjct: 101 ----KLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSR 136
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 112 bits (280), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 54/114 (47%), Positives = 75/114 (65%), Gaps = 2/114 (1%)
Query: 86 MEQNAQGRGDEPNRILLVTIHHMLYPITVEVLHQVFSPHGFVEKIVTFQKSAGFQALIQY 145
M+ G P +L + + ++ YP+T++VLHQ+FS G V KI+TF K+ FQAL+QY
Sbjct: 21 MDAGMAMAGQSP--VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQY 78
Query: 146 QLRPSAVVARSSLQGRNIYDGCCQLDIQFSNLDELQVNYNNERSRDFTNPNLPA 199
SA A+ SL G+NIY+ CC L I FS L L V YNN++SRD+T P+LP+
Sbjct: 79 ADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPS 132
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 16/100 (16%)
Query: 3 EPSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKN--QALLQMQDVPSAINALQF 60
P I V N+ + ++ + L Q+F FG + K++ N QALLQ D SA +A
Sbjct: 31 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHA--- 87
Query: 61 YTNVQPTIRGRNVY-------VQFSSHQELTTMEQNAQGR 93
+ ++ G+N+Y + FS L N + R
Sbjct: 88 ----KLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSR 123
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 112 bits (279), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 53/106 (50%), Positives = 73/106 (68%), Gaps = 2/106 (1%)
Query: 94 GDEPNRILLVTIHHMLYPITVEVLHQVFSPHGFVEKIVTFQKSAGFQALIQYQLRPSAVV 153
G P +L + + ++ YP+T++VLHQ+FS G V KI+TF K+ FQAL+QY SA
Sbjct: 24 GQSP--VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQH 81
Query: 154 ARSSLQGRNIYDGCCQLDIQFSNLDELQVNYNNERSRDFTNPNLPA 199
A+ SL G+NIY+ CC L I FS L L V YNN++SRD+T P+LP+
Sbjct: 82 AKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPS 127
Score = 33.9 bits (76), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 16/100 (16%)
Query: 3 EPSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKN--QALLQMQDVPSAINALQF 60
P I V N+ + ++ + L Q+F FG + K++ N QALLQ D SA +A
Sbjct: 26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHA--- 82
Query: 61 YTNVQPTIRGRNVY-------VQFSSHQELTTMEQNAQGR 93
+ ++ G+N+Y + FS L N + R
Sbjct: 83 ----KLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSR 118
>pdb|3TO8|A Chain A, Crystal Structure Of The Two C-Terminal Rrm Domains Of
Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 218
Score = 86.7 bits (213), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 54/182 (29%), Positives = 93/182 (51%), Gaps = 17/182 (9%)
Query: 252 DRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFL 311
D ++V L+ +++ D++FN+F LYGN+ ++K +++KP A+V+M DG+ + A+ L
Sbjct: 9 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 68
Query: 312 KGALLFGKRLEVNFSKHPNITQG---------ADTHEYMNSNLNRFN--RNAAKNYRYCC 360
+FG++L V SK P I G ++ S NRF+ AAKN
Sbjct: 69 NNNFMFGQKLNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ-- 126
Query: 361 SPTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQ----ALVLFETEEQATE 416
P+ ++H P +VTEE +E G + + +GK + L+ +E++ A E
Sbjct: 127 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPSSVKVFSGKSERSSSGLLEWESKSDALE 186
Query: 417 AL 418
L
Sbjct: 187 TL 188
>pdb|2E5I|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Heterogeneous Nuclear Ribonucleoprotein L-Like
Length = 124
Score = 86.7 bits (213), Expect = 2e-17, Method: Composition-based stats.
Identities = 44/109 (40%), Positives = 72/109 (66%), Gaps = 4/109 (3%)
Query: 92 GRGDEP---NRILLVTIHHMLYPITVEVLHQVFSPHGFVEKIVTFQKSAGFQALIQYQLR 148
G D+P N++LL++I + LYPITV+VL+ V +P G V++IV F+++ G QA+++++
Sbjct: 14 GNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESV 72
Query: 149 PSAVVARSSLQGRNIYDGCCQLDIQFSNLDELQVNYNNERSRDFTNPNL 197
A A+++L G +IY GCC L I+++ L V N+ S D+T P L
Sbjct: 73 LCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYL 121
>pdb|3TYT|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein L (Hnrpl) From Mus Musculus At 1.60 A
Resolution
Length = 205
Score = 86.3 bits (212), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 53/182 (29%), Positives = 93/182 (51%), Gaps = 17/182 (9%)
Query: 252 DRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFL 311
D ++V L+ +++ D++FN+F LYGN+ ++K +++KP A+V+M DG+ + A+ L
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62
Query: 312 KGALLFGKRLEVNFSKHPNITQG---------ADTHEYMNSNLNRFN--RNAAKNYRYCC 360
+FG+++ V SK P I G ++ S NRF+ AAKN
Sbjct: 63 NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ-- 120
Query: 361 SPTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQ----ALVLFETEEQATE 416
P+ ++H P +VTEE +E G T + +GK + L+ ++++ A E
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 417 AL 418
L
Sbjct: 181 TL 182
>pdb|2AD9|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd1 Complexed With Cucucu Rna
Length = 119
Score = 85.1 bits (209), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 37/90 (41%), Positives = 61/90 (67%)
Query: 4 PSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINALQFYTN 63
PS+VIH+R + +++E +++ L PFG +T L+ML+ KNQA ++M +A + +YT+
Sbjct: 30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTS 89
Query: 64 VQPTIRGRNVYVQFSSHQELTTMEQNAQGR 93
V P +RG+ +Y+QFS+H+EL T Q R
Sbjct: 90 VTPVLRGQPIYIQFSNHKELKTDSSPNQAR 119
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 357 RYCCSPTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQALVLFETEEQATE 416
R P+++IH+ LP DVTE E++S G + N L + GK QA + TEE A
Sbjct: 25 RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN--LLMLKGKNQAFIEMNTEE-AAN 81
Query: 417 ALVCKHAS---SLGGSIIRISFSQLQSIRENS 445
+V + S L G I I FS + ++ +S
Sbjct: 82 TMVNYYTSVTPVLRGQPIYIQFSNHKELKTDS 113
>pdb|1SJQ|A Chain A, Nmr Structure Of Rrm1 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 105
Score = 85.1 bits (209), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 37/91 (40%), Positives = 61/91 (67%)
Query: 4 PSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINALQFYTN 63
PS+VIH+R + +++E +++ L PFG +T L+ML+ KNQA ++M +A + +YT+
Sbjct: 15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTS 74
Query: 64 VQPTIRGRNVYVQFSSHQELTTMEQNAQGRG 94
V P +RG+ +Y+QFS+H+EL T Q R
Sbjct: 75 VTPVLRGQPIYIQFSNHKELKTDSSPNQARA 105
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 46/87 (52%), Gaps = 6/87 (6%)
Query: 362 PTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQALVLFETEEQATEALVCK 421
P+++IH+ LP DVTE E++S G + N L + GK QA + TEE A +V
Sbjct: 15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTN--LLMLKGKNQAFIEMNTEE-AANTMVNY 71
Query: 422 HAS---SLGGSIIRISFSQLQSIRENS 445
+ S L G I I FS + ++ +S
Sbjct: 72 YTSVTPVLRGQPIYIQFSNHKELKTDS 98
>pdb|2CQ1|A Chain A, Solution Structure Of Rna Binding Domain In Ptb-Like
Protein L
Length = 101
Score = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 32/82 (39%), Positives = 58/82 (70%)
Query: 4 PSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINALQFYTN 63
PS+V+H+R + E++E +++ L PFG +T ++ML+ KNQA L++ +AI + +Y+
Sbjct: 14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSA 73
Query: 64 VQPTIRGRNVYVQFSSHQELTT 85
V P +R + +Y+Q+S+H+EL T
Sbjct: 74 VTPHLRNQPIYIQYSNHKELKT 95
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 361 SPTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQALVLFETEEQA 414
+P++++H+ LP +VTE E+++ G + N + + GK QA + TEE A
Sbjct: 13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTN--ILMLKGKNQAFLELATEEAA 64
>pdb|3S01|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein L (Hnrpl) From Mus Musculus At 2.15 A
Resolution
Length = 212
Score = 75.9 bits (185), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 86/182 (47%), Gaps = 17/182 (9%)
Query: 252 DRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFL 311
D + V L+ + + D++FN+F LYGN+ ++K ++KP A V+ DG+ + A+ L
Sbjct: 3 DSPVLXVYGLDQSKXNCDRVFNVFCLYGNVEKVKFXKSKPGAAXVEXADGYAVDRAITHL 62
Query: 312 KGALLFGKRLEVNFSKHPNITQG---------ADTHEYMNSNLNRFN--RNAAKNYRYCC 360
FG++ V SK P I G ++ S NRF+ AAKN
Sbjct: 63 NNNFXFGQKXNVCVSKQPAIXPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ-- 120
Query: 361 SPTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQ----ALVLFETEEQATE 416
P+ ++H P +VTEE +E G T + +GK + L+ ++++ A E
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 417 AL 418
L
Sbjct: 181 TL 182
>pdb|3R27|A Chain A, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
pdb|3R27|B Chain B, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 100
Score = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 50/83 (60%)
Query: 2 TEPSKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINALQFY 61
T S V+H+R + + E DL++ Q FG I+ +V++ K QAL++ +DV A NA+ +
Sbjct: 18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYA 77
Query: 62 TNVQPTIRGRNVYVQFSSHQELT 84
+ Q I G +V +S+ Q+++
Sbjct: 78 ADNQIYIAGHPAFVNYSTSQKIS 100
>pdb|1WEX|A Chain A, Solution Structure Of Rrm Domain In Protein Bab28521
Length = 104
Score = 52.4 bits (124), Expect = 5e-07, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 46/80 (57%)
Query: 5 SKVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINALQFYTNV 64
S V+HVR + + E DL++ + FG I ++M+ K QAL++ +++ SA + F +V
Sbjct: 15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADV 74
Query: 65 QPTIRGRNVYVQFSSHQELT 84
I G+ + +S+ + +T
Sbjct: 75 PVYIAGQQAFFNYSTSKRIT 94
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 361 SPTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQALVLFETEEQATEAL 418
S + ++H+ L + V E ++V LE+ G+I + M K+QALV FE + A E +
Sbjct: 13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM--MPFKRQALVEFENIDSAKECV 68
>pdb|1X4D|A Chain A, Solution Structure Of Rrm Domain In Matrin 3
Length = 102
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 2 TEPSKVIHVRNV--GHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINALQ 59
E +V+H+ + G + LLQL +PFGVI+ ++L N+A ++M A A+
Sbjct: 12 VETRRVVHIMDFQRGKNL-RYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVD 70
Query: 60 FYTNVQPTIRGRNVYVQFS 78
+YT + G+ V V S
Sbjct: 71 YYTTTPALVFGKPVRVHLS 89
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 3 EPSKVIHVRNVGHE-ISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINALQFY 61
E +VIH+ N+ H S++ +L+L +P+G I +++R K+QA ++M+ A+ +
Sbjct: 23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHC 82
Query: 62 TNVQPTIRGRNVYVQFS 78
+GR V V S
Sbjct: 83 LKKALWFQGRCVKVDLS 99
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 2/86 (2%)
Query: 243 LPPGITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGF 302
L PG RC + V NL +D I E+ LF YG + + R++ +++
Sbjct: 12 LKPGEKTYTQRCRLFVGNLPTD-ITEEDFKRLFERYGEPSEVFINRDR-GFGFIRLESRT 69
Query: 303 QAELAVHFLKGALLFGKRLEVNFSKH 328
AE+A L G +L + L + F+ H
Sbjct: 70 LAEIAKAELDGTILKSRPLRIRFATH 95
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 29/151 (19%), Positives = 68/151 (45%), Gaps = 26/151 (17%)
Query: 8 IHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSA-INALQFYTNVQP 66
+ V N+ +I+E D +LF+ +G +++ + R + ++++ A I + +
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTI-- 82
Query: 67 TIRGRNVYVQFSSHQELTTMEQNAQGRGDEPNRILLVTIHHMLYPITVEVLHQVFSPHGF 126
++ R + ++F++H +T+ ++ ++ E+L Q FS G
Sbjct: 83 -LKSRPLRIRFATHG-------------------AALTVKNLSPVVSNELLEQAFSQFGP 122
Query: 127 VEK---IVTFQKSAGFQALIQYQLRPSAVVA 154
VEK +V + A + +++ +P A A
Sbjct: 123 VEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 254 CTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFLKG 313
C V V NL ++ ++ +L F YG + + + RN P A V+ D A AV L G
Sbjct: 74 CKVYVGNLGNNG-NKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132
Query: 314 ALLFGKRLEVNFS 326
L G R+ V S
Sbjct: 133 RTLCGCRVRVELS 145
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 254 CTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFLKG 313
C V V NL ++ ++ +L F YG + + + RN P A V+ D A AV L G
Sbjct: 74 CKVYVGNLGNNG-NKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDG 132
Query: 314 ALLFGKRLEVNFS 326
L G R+ V S
Sbjct: 133 RTLCGCRVRVELS 145
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 36/172 (20%), Positives = 77/172 (44%), Gaps = 38/172 (22%)
Query: 256 VLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPD-----HALVQMGDGFQAELAVHF 310
++V+ L D D + L+ LF G I +++R+ +A V ++ A+
Sbjct: 6 LIVNYLPQDMTDRE-LYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 311 LKGALLFGKRLEVNFSKHPNITQGADTHEYMNSNLNRFNRNAAKNYRYCCSPTKMIHLST 370
L G + KRL+V++++ P DT+ ++++
Sbjct: 65 LNGITVRNKRLKVSYAR-PGGESIKDTN---------------------------LYVTN 96
Query: 371 LPQDVTEEEIVSHLEEHGSIVNTKLF--EMNGKKQ--ALVLFETEEQATEAL 418
LP+ +T++++ + ++GSIV + ++ G+ + A V + E+A EA+
Sbjct: 97 LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
>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 = 37.7 bits (86), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 362 PTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLF----EMNGKKQALVLFETEEQATEA 417
P+++++L ++P D TEE+I+ G ++N K+ K A + F E + A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 418 LVCKHASSLGGSIIRISFSQLQSI 441
+ + LG ++ +S I
Sbjct: 62 VRNLNGYQLGSRFLKCGYSSNSDI 85
>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 = 37.7 bits (86), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 4/79 (5%)
Query: 362 PTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLF----EMNGKKQALVLFETEEQATEA 417
P+++++L ++P D TEE+I+ G ++N K+ K A + F E + A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 418 LVCKHASSLGGSIIRISFS 436
+ + LG ++ +S
Sbjct: 63 VRNLNGYQLGSRFLKCGYS 81
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 41/178 (23%), Positives = 79/178 (44%), Gaps = 43/178 (24%)
Query: 255 TVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNK-PDHALVQMGDGF-------QAEL 306
T L+ N + +D+L +LFS G + KL+R+K H+L G GF AE
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSL---GYGFVNYVTAKDAER 59
Query: 307 AVHFLKGALLFGKRLEVNFSKHPNITQGADTHEYMNSNLNRFNRNAAKNYRYCCSPTKMI 366
A++ L G L K ++V++++ + ++NL
Sbjct: 60 AINTLNGLRLQSKTIKVSYAR-------PSSEVIKDANL--------------------- 91
Query: 367 HLSTLPQDVTEEEIVSHLEEHGSIVNTKLF--EMNG--KKQALVLFETEEQATEALVC 420
++S LP+ +T++++ G I+N+++ + G + A + F+ +A EA+
Sbjct: 92 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 41/178 (23%), Positives = 79/178 (44%), Gaps = 43/178 (24%)
Query: 255 TVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNK-PDHALVQMGDGF-------QAEL 306
T L+ N + +D+L +LFS G + KL+R+K H+L G GF AE
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSL---GYGFVNYVTAKDAER 59
Query: 307 AVHFLKGALLFGKRLEVNFSKHPNITQGADTHEYMNSNLNRFNRNAAKNYRYCCSPTKMI 366
A++ L G L K ++V++++ + ++NL
Sbjct: 60 AINTLNGLRLQSKTIKVSYAR-------PSSEVIKDANL--------------------- 91
Query: 367 HLSTLPQDVTEEEIVSHLEEHGSIVNTKLF--EMNG--KKQALVLFETEEQATEALVC 420
++S LP+ +T++++ G I+N+++ + G + A + F+ +A EA+
Sbjct: 92 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 37.0 bits (84), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 362 PTKMIHLSTLPQDVTEEEIVSHL----EEHGSIVNTKLFEMNGKKQALVLFETEEQATEA 417
P K+++L L VTE ++VS E+ G + ++ + QA + F +E A +A
Sbjct: 24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 83
Query: 418 LVCKHASSLGGSIIRISFSQ 437
L + L G I+ I F +
Sbjct: 84 LHLVNGYKLYGKILVIEFGK 103
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 44/86 (51%), Gaps = 8/86 (9%)
Query: 3 EPSKVIHVRNVGHEISENDLLQLFQPF----GVITKLVML--RAKNQALLQMQDVPSAIN 56
EP+KV++++N+ ++E DL+ LF F G + M+ R + QA + + A
Sbjct: 23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 57 ALQFYTNVQPTIRGRNVYVQFSSHQE 82
AL + + G+ + ++F +++
Sbjct: 83 ALHLVNGYK--LYGKILVIEFGKNKK 106
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 256 VLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFLKGAL 315
V V NL + + +L FS YG + + + RN P A V+ D AE AV L G +
Sbjct: 3 VYVGNLGTG-AGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 316 LFGKRLEVNFS 326
+ G R+ V S
Sbjct: 62 ICGSRVRVELS 72
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 4/79 (5%)
Query: 362 PTKMIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLF----EMNGKKQALVLFETEEQATEA 417
P+++++L ++P D TEE+I+ G ++N K+ K A + F E + A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 418 LVCKHASSLGGSIIRISFS 436
+ + LG ++ +S
Sbjct: 61 VRNLNGYQLGSRFLKCGYS 79
>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 = 35.8 bits (81), Expect = 0.056, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 4/85 (4%)
Query: 356 YRYCCSPTK-MIHLSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQ---ALVLFETE 411
+RY S K + +S LP T+EE+ + HG++ + +L K A V +E E
Sbjct: 9 FRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENE 68
Query: 412 EQATEALVCKHASSLGGSIIRISFS 436
QA++A++ ++ +II+++ S
Sbjct: 69 SQASQAVMKMDGMTIKENIIKVAIS 93
>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 = 35.0 bits (79), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 36/172 (20%), Positives = 76/172 (44%), Gaps = 38/172 (22%)
Query: 256 VLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPD-----HALVQMGDGFQAELAVHF 310
++V+ L D D + L+ LF G I ++ R+ +A V ++ A+
Sbjct: 17 LIVNYLPQDXTDRE-LYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 311 LKGALLFGKRLEVNFSKHPNITQGADTHEYMNSNLNRFNRNAAKNYRYCCSPTKMIHLST 370
L G + KRL+V++++ P DT+ ++++
Sbjct: 76 LNGITVRNKRLKVSYAR-PGGESIKDTN---------------------------LYVTN 107
Query: 371 LPQDVTEEEIVSHLEEHGSIVNTKLF--EMNGKKQ--ALVLFETEEQATEAL 418
LP+ +T++++ + ++GSIV + ++ G+ + A V + E+A EA+
Sbjct: 108 LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 7/87 (8%)
Query: 247 ITGTND----RCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGF 302
+T ND V + NLN+ + + + +FS YG + + + +A VQ +
Sbjct: 17 VTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG---YAFVQYSNER 73
Query: 303 QAELAVHFLKGALLFGKRLEVNFSKHP 329
A AV G +L G+ L++N + P
Sbjct: 74 HARAAVLGENGRVLAGQTLDINMAGEP 100
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 18 SENDLLQLFQPFGVITKLVMLRAKN 42
SE D+L+LFQPFGVI + +LR +
Sbjct: 28 SEEDVLRLFQPFGVIDECTVLRGPD 52
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 32.7 bits (73), Expect = 0.46, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 8 IHVRNVGHEISENDLLQLFQPFGVITKLVMLRAK 41
I V N+ + E DL +LF+PFG I+++ + + K
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK 51
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 257 LVSNLNSDRIDEDKLFNLFSLYGNIIRIKLL-----RNKPDHALVQMGDGFQAELAVHFL 311
L+ N +DE +L LF YG I +K++ R + V+ G A+ A+ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 312 KGALLFGKRLEVNFS 326
G + KRL+V +
Sbjct: 105 NGFNILNKRLKVALA 119
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 32.3 bits (72), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 35/176 (19%), Positives = 77/176 (43%), Gaps = 37/176 (21%)
Query: 252 DRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPD-----HALVQMGDGFQAEL 306
D T L+ N + +D+ +LF G+I KL+R+K + V D A+
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 307 AVHFLKGALLFGKRLEVNFSKHPNITQGADTHEYMNSNLNRFNRNAAKNYRYCCSPTKMI 366
A++ L G L K ++V++++ + ++NL
Sbjct: 62 AINTLNGLKLQTKTIKVSYAR-------PSSASIRDANL--------------------- 93
Query: 367 HLSTLPQDVTEEEIVSHLEEHGSIVNTKLF--EMNGKKQAL--VLFETEEQATEAL 418
++S LP+ ++++E+ ++G I+ +++ + G + + + F+ +A EA+
Sbjct: 94 YVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.3 bits (72), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 2/84 (2%)
Query: 245 PGITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQA 304
PG R + V NL D I E+++ LF YG + + ++K +++ A
Sbjct: 14 PGEKTFTQRSRLFVGNLPPD-ITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLA 71
Query: 305 ELAVHFLKGALLFGKRLEVNFSKH 328
E+A L L GK+L V F+ H
Sbjct: 72 EIAKVELDNMPLRGKQLRVRFACH 95
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.3 bits (72), Expect = 0.57, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 246 GITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAE 305
G +G + V NL ++ + E+ L FS +G + R+K L+ D+A + + A
Sbjct: 4 GSSGMAKVKVLFVRNL-ANTVTEEILEKAFSQFGKLERVKKLK---DYAFIHFDERDGAV 59
Query: 306 LAVHFLKGALLFGKRLEVNFSKHPN 330
A+ + G L G+ +E+ F+K P+
Sbjct: 60 KAMEEMNGKDLEGENIEIVFAKPPD 84
Score = 31.6 bits (70), Expect = 0.99, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 6 KVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINALQFYTNVQ 65
KV+ VRN+ + ++E L + F FG + ++ L K+ A + + A+ A++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNG-- 67
Query: 66 PTIRGRNVYVQFSSHQELTTMEQNAQ 91
+ G N+ + F+ + E+ AQ
Sbjct: 68 KDLEGENIEIVFAKPPDQKRKERKAQ 93
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 31.6 bits (70), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 11/81 (13%)
Query: 255 TVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNK-PDHALVQMGDGF-------QAEL 306
T L+ N + +D+L +LFS G + KL+R+K H+L G GF AE
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSL---GYGFVNYVTAKDAER 61
Query: 307 AVHFLKGALLFGKRLEVNFSK 327
A++ L G L K ++V++++
Sbjct: 62 AINTLNGLRLQSKTIKVSYAR 82
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 31.6 bits (70), Expect = 0.87, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 256 VLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFLKGAL 315
V + NLN+ + + + +FS YG I+ + + A VQ + A AV G +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG---FAFVQYVNERNARAAVAGEDGRM 74
Query: 316 LFGKRLEVNFSKHPNITQ 333
+ G+ L++N + P + +
Sbjct: 75 IAGQVLDINLAAEPKVNR 92
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 9/91 (9%)
Query: 241 GGLPPGITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHA----LV 296
G L G G+ TV V+NL+ ++ KL +FS+ G ++R +L +K + V
Sbjct: 7 GALQAGRLGS----TVFVANLDY-KVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTV 61
Query: 297 QMGDGFQAELAVHFLKGALLFGKRLEVNFSK 327
+A A+ G LLF + + V +
Sbjct: 62 TFEQSIEAVQAISMFNGQLLFDRPMHVKMDE 92
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 35/173 (20%), Positives = 76/173 (43%), Gaps = 37/173 (21%)
Query: 255 TVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPD-----HALVQMGDGFQAELAVH 309
T L+ N + +++ +LF G I KL+R+K + V D AE A++
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 310 FLKGALLFGKRLEVNFSKHPNITQGADTHEYMNSNLNRFNRNAAKNYRYCCSPTKMIHLS 369
L G L K ++V++++ + ++NL ++S
Sbjct: 63 TLNGLRLQTKTIKVSYAR-------PSSASIRDANL---------------------YVS 94
Query: 370 TLPQDVTEEEIVSHLEEHGSIVNTKLF--EMNGKKQAL--VLFETEEQATEAL 418
LP+ +T++E+ ++G I+ +++ ++ G + + + F+ +A EA+
Sbjct: 95 GLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 253 RCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDH-----ALVQMGDGFQAELA 307
+ TV VSNL + D L+ +FS YG ++++ ++++K A + D A+
Sbjct: 16 KSTVYVSNLPFSLTNND-LYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 308 VHFLKGALLFGKRLEVNFS 326
+ LFG+ ++ + +
Sbjct: 75 TRAINNKQLFGRVIKASIA 93
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 7/84 (8%)
Query: 249 GTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPD------HALVQMGDGF 302
G++ + + NL+ + IDE L++ FS +G I++ + PD +A +
Sbjct: 1 GSSGSSGIFIGNLDPE-IDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFD 59
Query: 303 QAELAVHFLKGALLFGKRLEVNFS 326
++ A+ + G L + + V+++
Sbjct: 60 ASDAAIEAMNGQYLCNRPITVSYA 83
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 242 GLPPGITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDG 301
GL P G++ + + + NL + ++ LF +FS YG+I++I + K +Q +
Sbjct: 13 GLVP--RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNP 67
Query: 302 FQAELAVHFLKGALLFGKRL 321
A+ + FGK+L
Sbjct: 68 QSVRDAIEXESQEMNFGKKL 87
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 11/81 (13%)
Query: 255 TVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNK-PDHALVQMGDGF-------QAEL 306
T L+ N +D+L +LFS G + KL+R+K H+L G GF AE
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSL---GYGFVNYVTAKDAER 76
Query: 307 AVHFLKGALLFGKRLEVNFSK 327
A++ L G L K ++V++++
Sbjct: 77 AINTLNGLRLQSKTIKVSYAR 97
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 242 GLPPGITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDG 301
GL P G++ + + + NL + ++ LF +FS YG+I++I + K +Q +
Sbjct: 13 GLVP--RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNP 67
Query: 302 FQAELAVHFLKGALLFGKRL 321
A+ + FGK+L
Sbjct: 68 QSVRDAIECESQEMNFGKKL 87
>pdb|3EAP|A Chain A, Crystal Structure Of The Rhogap Domain Of Arhgap11a
pdb|3EAP|B Chain B, Crystal Structure Of The Rhogap Domain Of Arhgap11a
pdb|3EAP|C Chain C, Crystal Structure Of The Rhogap Domain Of Arhgap11a
pdb|3EAP|D Chain D, Crystal Structure Of The Rhogap Domain Of Arhgap11a
Length = 271
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 8/43 (18%)
Query: 252 DRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHA 294
D CT L +++++ LF G++IR+K L+NK DH
Sbjct: 89 DACTSLEDHIHTE--------GLFRKSGSVIRLKALKNKVDHG 123
>pdb|2NYF|A Chain A, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Nostoc Punctiforme
Length = 567
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 239 FGGGLPPGITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHA 294
F GLPP + G +DR + L +I + + L S YGN L P HA
Sbjct: 396 FSNGLPPSLVGNSDRKVNM--GLKGLQISGNSIMPLLSFYGN----SLADRFPTHA 445
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 29.3 bits (64), Expect = 4.3, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 252 DRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPD-----HALVQMGDGFQAEL 306
D T L+ N + +D+ +LF G+I KL+R+K + V D A+
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 307 AVHFLKGALLFGKRLEVNFSK 327
A++ L G L K ++V++++
Sbjct: 62 AINTLNGLKLQTKTIKVSYAR 82
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.3 bits (64), Expect = 4.4, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 6 KVIHVRNVGHEISENDLLQLFQPFGVITKLVMLRAKNQALLQMQDVPSAINAL 58
KV+ VRN+ ++E L + F FG + ++ L K+ A + +D +A+ A+
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKL--KDYAFVHFEDRGAAVKAM 66
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 29.3 bits (64), Expect = 4.5, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 8 IHVRNVGHEISENDLLQLFQPFGVITKLVML------RAKNQALLQMQDVPSAINALQFY 61
I V + H E +L + F+ FGV+T++VM+ R + + +D S A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 62 TNVQPTIRGRNVYVQ 76
+ I G+ V V+
Sbjct: 73 FH---DIMGKKVEVK 84
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 246 GITGTNDRCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAE 305
G +G++ + + NL + E ++ +LF YG ++ +++N + V + D AE
Sbjct: 1 GSSGSSGMVKLFIGNLPREAT-EQEIRSLFEQYGKVLECDIIKN---YGFVHIEDKTAAE 56
Query: 306 LAVHFLKGALLFGKRLEVNFSK 327
A+ L L G + V SK
Sbjct: 57 DAIRNLHHYKLHGVNINVEASK 78
Score = 28.9 bits (63), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 368 LSTLPQDVTEEEIVSHLEEHGSIVNTKLFEMNGKKQALVLFETEEQATEALVCKHASSLG 427
+ LP++ TE+EI S E++G ++ + K V E + A +A+ H L
Sbjct: 13 IGNLPREATEQEIRSLFEQYGKVLECDII----KNYGFVHIEDKTAAEDAIRNLHHYKLH 68
Query: 428 GSIIRISFSQLQS 440
G I + S+ +S
Sbjct: 69 GVNINVEASKNKS 81
>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 = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 366 IHLSTLPQDVTEEEIVSHLEEHGSIVNTKLF--EMNGKKQ--ALVLFETEEQATEAL 418
++++ LP+ +T++++ + ++GSIV + ++ G+ + A V + E+A EA+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 253 RCTVLVSNLNSDRIDEDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVHFLK 312
+ + + NL + ++ LF +FS YG+I++I + K +Q + A+
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECES 66
Query: 313 GALLFGKRL 321
+ FGK+L
Sbjct: 67 QEMNFGKKL 75
>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 = 28.5 bits (62), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 22/102 (21%), Positives = 50/102 (49%), Gaps = 13/102 (12%)
Query: 72 NVYVQFSSHQELTTMEQNAQGRGDEPNRIL----LVTIHHMLYPITVEVLHQVFSPHGFV 127
+ YV+ S +++ Q+ +G +E ++L + + ++ + T E ++++FS G +
Sbjct: 12 DSYVELSQYRD-----QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66
Query: 128 EKIV----TFQKSAGFQALIQYQLRPSAVVARSSLQGRNIYD 165
+KI+ +K+A ++Y R A A + G + D
Sbjct: 67 KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD 108
>pdb|2D9O|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj10634
Length = 100
Score = 28.1 bits (61), Expect = 9.8, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 268 EDKLFNLFSLYGNIIRIKLLRNKPDHALVQMGDGFQAELAVH 309
+D L L YG ++ + L KP A+V+ AELAV
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQ 72
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.134 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,584,070
Number of Sequences: 62578
Number of extensions: 503858
Number of successful extensions: 1394
Number of sequences better than 100.0: 61
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 1319
Number of HSP's gapped (non-prelim): 97
length of query: 446
length of database: 14,973,337
effective HSP length: 102
effective length of query: 344
effective length of database: 8,590,381
effective search space: 2955091064
effective search space used: 2955091064
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)