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= 024708
(264 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 109 bits (272), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 58/117 (49%), Positives = 75/117 (64%), Gaps = 1/117 (0%)
Query: 52 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 111
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 37 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 96
Query: 112 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTPMVNSQPSI 168
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P +SQPS+
Sbjct: 97 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSL 152
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 4 CTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS--AIDASGQLSVGL 50
CTLRI +S T L+VK+ + +SRDYT P LP S ++D + + GL
Sbjct: 114 CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAFGL 162
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 108 bits (271), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 58/117 (49%), Positives = 75/117 (64%), Gaps = 1/117 (0%)
Query: 52 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 111
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 24 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 83
Query: 112 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTPMVNSQPSI 168
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P +SQPS+
Sbjct: 84 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSL 139
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 4 CTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 38
CTLRI +S T L+VK+ + +SRDYT P LP S
Sbjct: 101 CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 135
>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 = 102 bits (253), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 54/109 (49%), Positives = 69/109 (63%), Gaps = 1/109 (0%)
Query: 52 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 111
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 19 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 78
Query: 112 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTP 160
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P
Sbjct: 79 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLP 126
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 4 CTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 38
CTLRI +S T L+VK+ + +SRDYT P LP S
Sbjct: 96 CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 130
>pdb|2E5I|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Heterogeneous Nuclear Ribonucleoprotein L-Like
Length = 124
Score = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 44/99 (44%), Positives = 63/99 (63%), Gaps = 2/99 (2%)
Query: 59 SNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEA 118
+ VLL SI+N Y +T+DVL+ V + G VQ+I +F +N G+QA++++ V A AK A
Sbjct: 23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAA 81
Query: 119 LEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLP 157
L G IY G C L I Y+R T L++ N++ S DYT P
Sbjct: 82 LNGADIY-AGCCTLKIEYARPTRLNVIRNDNDSWDYTKP 119
Score = 34.3 bits (77), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 20/32 (62%)
Query: 2 GPCTLRITYSAHTDLSVKFQSHRSRDYTNPYL 33
G CTL+I Y+ T L+V + S DYT PYL
Sbjct: 90 GCCTLKIEYARPTRLNVIRNDNDSWDYTKPYL 121
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 66 IENMQYAVTLDVLHMVFSAFGPVQKIA-MFDKNGG--LQALIQYPDVQTAVVAKEALEGH 122
+ N+ A+T D+L F GP+ I M DKN A ++Y A +A + L G
Sbjct: 5 VGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGK 64
Query: 123 CIYDGGFCKLHISY 136
I + K++ ++
Sbjct: 65 QI-ENNIVKINWAF 77
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 66 IENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQAL-------IQYPDVQTAVVAKEA 118
I+N+ ++ T + L VFS G ++ + K L ++Y + A A +
Sbjct: 10 IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 69
Query: 119 LEGHCIYDGGFCKLHIS 135
L+GH + DG ++ IS
Sbjct: 70 LQGHTV-DGHKLEVRIS 85
>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 = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 35/135 (25%), Positives = 58/135 (42%), Gaps = 8/135 (5%)
Query: 6 LRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPSAIDASGQLSVGLDGKKLEPESNVLLAS 65
+RIT S H ++ + + + T Y G + + + P S L
Sbjct: 102 IRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF----QNIFPPSATL--H 155
Query: 66 IENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGHCIY 125
+ N+ +V+ + L ++FS+ G V K F + ALIQ V+ AV A L H +
Sbjct: 156 LSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL- 214
Query: 126 DGGFCKLHISYSRHT 140
G L +S+S+ T
Sbjct: 215 -GENHHLRVSFSKST 228
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 65 SIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGHCI 124
+++N+ V+ ++L FS FGPV+K + + G + + A++ALE C
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE-RC- 157
Query: 125 YDGGF 129
DG F
Sbjct: 158 GDGAF 162
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 66 IENMQYAVTLDVLHMVFSAFGPVQKIAM-FDKNGGL---QALIQYPDVQTAVVAKEALEG 121
+ N+ Y T + L +FS GPV + +D+ G +Y D +TA+ A L G
Sbjct: 13 VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNG 72
Query: 122 H 122
Sbjct: 73 R 73
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 33 LPVAPSAIDASG--QLSVGLDGKKLEPES-NVLLASIENMQYAVTLDVLHMVFSAFGP-- 87
LP ++ DASG Q V L +LE L ASI N+Q +L + + SA GP
Sbjct: 166 LPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAI 225
Query: 88 --VQKIAMFDKNGGLQALIQYPDV 109
+ K+ D G AL YP +
Sbjct: 226 HHLPKLEELDLR-GCTALRNYPPI 248
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 66 IENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGHCIY 125
+ N+ +V+ + L ++FS+ G V K F + ALIQ V+ AV A L H +
Sbjct: 125 LSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL- 183
Query: 126 DGGFCKLHISYSRHT 140
G L +S+S+ T
Sbjct: 184 -GENHHLRVSFSKST 197
>pdb|4A69|A Chain A, Structure Of Hdac3 Bound To Corepressor And Inositol
Tetraphosphate
pdb|4A69|B Chain B, Structure Of Hdac3 Bound To Corepressor And Inositol
Tetraphosphate
Length = 376
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 110 QTAVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDY-------TLPSTPMV 162
+T+++ +EA+ Y F ++ H D+S ++ N SR Y + M+
Sbjct: 310 ETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKML 369
Query: 163 NSQPSI 168
N PS+
Sbjct: 370 NHAPSV 375
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 0.132 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,665,944
Number of Sequences: 62578
Number of extensions: 237275
Number of successful extensions: 462
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 445
Number of HSP's gapped (non-prelim): 19
length of query: 264
length of database: 14,973,337
effective HSP length: 97
effective length of query: 167
effective length of database: 8,903,271
effective search space: 1486846257
effective search space used: 1486846257
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: 50 (23.9 bits)