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= 020065
(331 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: 119 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 178
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 37 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 96
Query: 179 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTPMVNSQPSI 235
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P +SQPS+
Sbjct: 97 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSL 152
Score = 79.3 bits (194), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 43/91 (47%), Positives = 56/91 (61%), Gaps = 7/91 (7%)
Query: 15 QVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLR 74
Q+FS FG V KI TF K FQAL+Q++D +A AK +LDG++I CTLR
Sbjct: 65 QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN-------ACCTLR 117
Query: 75 ITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 105
I +S T L+VK+ + +SRDYT P LP S
Sbjct: 118 IDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 148
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 108 bits (270), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 58/117 (49%), Positives = 75/117 (64%), Gaps = 1/117 (0%)
Query: 119 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 178
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 24 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 83
Query: 179 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTPMVNSQPSI 235
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P +SQPS+
Sbjct: 84 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSL 139
Score = 78.6 bits (192), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 43/91 (47%), Positives = 56/91 (61%), Gaps = 7/91 (7%)
Query: 15 QVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLR 74
Q+FS FG V KI TF K FQAL+Q++D +A AK +LDG++I CTLR
Sbjct: 52 QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN-------ACCTLR 104
Query: 75 ITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 105
I +S T L+VK+ + +SRDYT P LP S
Sbjct: 105 IDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 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 = 101 bits (252), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 54/109 (49%), Positives = 69/109 (63%), Gaps = 1/109 (0%)
Query: 119 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 178
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 19 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 78
Query: 179 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTP 227
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P
Sbjct: 79 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLP 126
Score = 79.0 bits (193), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 43/91 (47%), Positives = 56/91 (61%), Gaps = 7/91 (7%)
Query: 15 QVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLR 74
Q+FS FG V KI TF K FQAL+Q++D +A AK +LDG++I CTLR
Sbjct: 47 QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN-------ACCTLR 99
Query: 75 ITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 105
I +S T L+VK+ + +SRDYT P LP S
Sbjct: 100 IDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 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 = 3e-15, Method: Compositional matrix adjust.
Identities = 49/120 (40%), Positives = 69/120 (57%), Gaps = 11/120 (9%)
Query: 114 SVGLDGKKLEPESN---------VLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKN 164
S G GK++ N VLL SI+N Y +T+DVL+ V + G VQ+I +F +N
Sbjct: 2 SSGSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN 61
Query: 165 GGLQALIQYPDVQTAVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLP 224
G+QA++++ V A AK AL G IY G C L I Y+R T L++ N++ S DYT P
Sbjct: 62 -GIQAMVEFESVLCAQKAKAALNGADIY-AGCCTLKIEYARPTRLNVIRNDNDSWDYTKP 119
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 47/93 (50%), Gaps = 8/93 (8%)
Query: 8 LKVIFILQVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPEN 67
+ V + V + G V +I F++ G QA+V+F A AK AL+G I
Sbjct: 37 ITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAALNGADI-------Y 88
Query: 68 MGPCTLRITYSAHTDLSVKFQSHRSRDYTNPYL 100
G CTL+I Y+ T L+V + S DYT PYL
Sbjct: 89 AGCCTLKIEYARPTRLNVIRNDNDSWDYTKPYL 121
>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 = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 52/198 (26%), Positives = 83/198 (41%), Gaps = 22/198 (11%)
Query: 11 IFILQVFSAFGFVHKITT-FEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMG 69
+FIL F +G V ++ F K ALVQ +D A A + L+G +
Sbjct: 52 LFIL--FGVYGDVQRVKILFNKKE--NALVQMADGNQAQLAMSHLNGHKLH--------- 98
Query: 70 PCTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPSAIDASGQLSVGLDGKKLEPESNVL 129
+RIT S H ++ + + + T Y G + + + P S L
Sbjct: 99 GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF----QNIFPPSATL 154
Query: 130 LASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGH 189
+ N+ +V+ + L ++FS+ G V K F + ALIQ V+ AV A L H
Sbjct: 155 --HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 212
Query: 190 CIYDGGFCKLHISYSRHT 207
+ G L +S+S+ T
Sbjct: 213 DL--GENHHLRVSFSKST 228
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 52/198 (26%), Positives = 83/198 (41%), Gaps = 22/198 (11%)
Query: 11 IFILQVFSAFGFVHKITT-FEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMG 69
+FIL F +G V ++ F K ALVQ +D A A + L+G +
Sbjct: 21 LFIL--FGVYGDVQRVKILFNKKEN--ALVQMADGNQAQLAMSHLNGHK---------LH 67
Query: 70 PCTLRITYSAHTDLSVKFQSHRSRDYTNPYLPVAPSAIDASGQLSVGLDGKKLEPESNVL 129
+RIT S H ++ + + + T Y G + + + P S L
Sbjct: 68 GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF----QNIFPPSATL 123
Query: 130 LASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGH 189
+ N+ +V+ + L ++FS+ G V K F + ALIQ V+ AV A L H
Sbjct: 124 --HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 181
Query: 190 CIYDGGFCKLHISYSRHT 207
+ G L +S+S+ T
Sbjct: 182 DL--GENHHLRVSFSKST 197
>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 = 0.57, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 133 IENMQYAVTLDVLHMVFSAFGPVQKIA-MFDKNGG--LQALIQYPDVQTAVVAKEALEGH 189
+ N+ A+T D+L F GP+ I M DKN A ++Y A +A + L G
Sbjct: 5 VGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGK 64
Query: 190 CIYDGGFCKLHISY 203
I + K++ ++
Sbjct: 65 QI-ENNIVKINWAF 77
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
Specific Factor 1 Variant
Length = 112
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 18 SAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGR 57
S FG + K+ F++ A V F D E A LDGR
Sbjct: 48 SKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGR 87
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 132 SIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGHCI 191
+++N+ V+ ++L FS FGPV+K + + G + + A++ALE C
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE-RC- 157
Query: 192 YDGGF 196
DG F
Sbjct: 158 GDGAF 162
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 100 LPVAPSAIDASGQLS--VGLDGKKLEPES-NVLLASIENMQYAVTLDVLHMVFSAFGP-- 154
LP ++ DASG+ V L +LE L ASI N+Q +L + + SA GP
Sbjct: 166 LPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAI 225
Query: 155 --VQKIAMFDKNGGLQALIQYPDV 176
+ K+ D G AL YP +
Sbjct: 226 HHLPKLEELDLR-GCTALRNYPPI 248
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 0.133 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,248,491
Number of Sequences: 62578
Number of extensions: 302319
Number of successful extensions: 557
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 534
Number of HSP's gapped (non-prelim): 24
length of query: 331
length of database: 14,973,337
effective HSP length: 99
effective length of query: 232
effective length of database: 8,778,115
effective search space: 2036522680
effective search space used: 2036522680
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: 52 (24.6 bits)