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= 019494
(340 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: 128 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 187
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 37 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 96
Query: 188 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTPMVNSQPSI 244
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P +SQPS+
Sbjct: 97 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSL 152
Score = 77.8 bits (190), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 42/91 (46%), Positives = 55/91 (60%), Gaps = 7/91 (7%)
Query: 24 HVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLR 83
+FS FG V KI TF K FQAL+Q++D +A AK +LDG++I CTLR
Sbjct: 65 QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN-------ACCTLR 117
Query: 84 ITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 114
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 (271), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 58/117 (49%), Positives = 75/117 (64%), Gaps = 1/117 (0%)
Query: 128 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 187
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 24 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 83
Query: 188 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTPMVNSQPSI 244
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P +SQPS+
Sbjct: 84 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSL 139
Score = 77.0 bits (188), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 42/91 (46%), Positives = 55/91 (60%), Gaps = 7/91 (7%)
Query: 24 HVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLR 83
+FS FG V KI TF K FQAL+Q++D +A AK +LDG++I CTLR
Sbjct: 52 QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN-------ACCTLR 104
Query: 84 ITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 114
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 = 102 bits (253), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 54/109 (49%), Positives = 69/109 (63%), Gaps = 1/109 (0%)
Query: 128 GKKLEPESNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQT 187
G + +S VL +EN+ Y VTLDVLH +FS FG V KI F KN QAL+QY D +
Sbjct: 19 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS 78
Query: 188 AVVAKEALEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLPSTP 236
A AK +L+G IY+ C L I +S+ T L++K NND+SRDYT P P
Sbjct: 79 AQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLP 126
Score = 77.0 bits (188), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 42/91 (46%), Positives = 55/91 (60%), Gaps = 7/91 (7%)
Query: 24 HVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLR 83
+FS FG V KI TF K FQAL+Q++D +A AK +LDG++I CTLR
Sbjct: 47 QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN-------ACCTLR 99
Query: 84 ITYSAHTDLSVKFQSHRSRDYTNPYLPVAPS 114
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 = 44/99 (44%), Positives = 63/99 (63%), Gaps = 2/99 (2%)
Query: 135 SNVLLASIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEA 194
+ VLL SI+N Y +T+DVL+ V + G VQ+I +F +N G+QA++++ V A AK A
Sbjct: 23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAA 81
Query: 195 LEGHCIYDGGFCKLHISYSRHTDLSIKVNNDRSRDYTLP 233
L G IY G C L I Y+R T L++ N++ S DYT P
Sbjct: 82 LNGADIY-AGCCTLKIEYARPTRLNVIRNDNDSWDYTKP 119
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 33/85 (38%), Positives = 44/85 (51%), Gaps = 8/85 (9%)
Query: 25 VFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLRI 84
V + G V +I F++ G QA+V+F A AK AL+G I G CTL+I
Sbjct: 45 VCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAALNGADI-------YAGCCTLKI 96
Query: 85 TYSAHTDLSVKFQSHRSRDYTNPYL 109
Y+ T L+V + S DYT PYL
Sbjct: 97 EYARPTRLNVIRNDNDSWDYTKPYL 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 = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 49/193 (25%), Positives = 80/193 (41%), Gaps = 20/193 (10%)
Query: 25 VFSAFGFVHKITT-FEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLR 83
+F +G V ++ F K ALVQ +D A A + L+G + +R
Sbjct: 55 LFGVYGDVQRVKILFNKKE--NALVQMADGNQAQLAMSHLNGHKLH---------GKPIR 103
Query: 84 ITYSAHTDLSVKFQSHRSRDYTNPYLPVAPSAIDASGQLSVGLDGKKLEPESNVLLASIE 143
IT S H ++ + + + T Y G + + + P S L +
Sbjct: 104 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF----QNIFPPSATL--HLS 157
Query: 144 NMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGHCIYDG 203
N+ +V+ + L ++FS+ G V K F + ALIQ V+ AV A L H + G
Sbjct: 158 NIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL--G 215
Query: 204 GFCKLHISYSRHT 216
L +S+S+ T
Sbjct: 216 ENHHLRVSFSKST 228
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 34.7 bits (78), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 49/193 (25%), Positives = 80/193 (41%), Gaps = 20/193 (10%)
Query: 25 VFSAFGFVHKITT-FEKTAGFQALVQFSDTETASSAKNALDGRSIPRYLLPENMGPCTLR 83
+F +G V ++ F K ALVQ +D A A + L+G + +R
Sbjct: 24 LFGVYGDVQRVKILFNKKEN--ALVQMADGNQAQLAMSHLNGHK---------LHGKPIR 72
Query: 84 ITYSAHTDLSVKFQSHRSRDYTNPYLPVAPSAIDASGQLSVGLDGKKLEPESNVLLASIE 143
IT S H ++ + + + T Y G + + + P S L +
Sbjct: 73 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF----QNIFPPSATL--HLS 126
Query: 144 NMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGHCIYDG 203
N+ +V+ + L ++FS+ G V K F + ALIQ V+ AV A L H + G
Sbjct: 127 NIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL--G 184
Query: 204 GFCKLHISYSRHT 216
L +S+S+ T
Sbjct: 185 ENHHLRVSFSKST 197
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 32.0 bits (71), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 142 IENMQYAVTLDVLHMVFSAFGPVQKIA-MFDKNGG--LQALIQYPDVQTAVVAKEALEGH 198
+ N+ A+T D+L F GP+ I M DKN A ++Y A +A + L G
Sbjct: 5 VGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGK 64
Query: 199 CI 200
I
Sbjct: 65 QI 66
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 6 PLSRKYLQWQLSASGERAHVFSAFGF---VHKITTFEKTAGFQALVQFSDTETASSAKNA 62
PL K L +G + + AFG+ + + GF A V+F D A+ A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGF-AFVEFEDPRDAADAVRE 129
Query: 63 LDGRSI 68
LDGR++
Sbjct: 130 LDGRTL 135
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 6 PLSRKYLQWQLSASGERAHVFSAFGF---VHKITTFEKTAGFQALVQFSDTETASSAKNA 62
PL K L +G + + AFG+ + + GF A V+F D A+ A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGF-AFVEFEDPRDAADAVRD 129
Query: 63 LDGRSI 68
LDGR++
Sbjct: 130 LDGRTL 135
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 17 SASGERAHVFSAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGRSI 68
+ GE FS +G + + GF A V+F D A A LDG+ I
Sbjct: 12 AGKGELERAFSYYGPLRTVWIARNPPGF-AFVEFEDPRDAEDAVRGLDGKVI 62
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 141 SIENMQYAVTLDVLHMVFSAFGPVQKIAMFDKNGGLQALIQYPDVQTAVVAKEALEGHCI 200
+++N+ V+ ++L FS FGPV+K + + G + + A++ALE C
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE-RC- 157
Query: 201 YDGGF 205
DG F
Sbjct: 158 GDGAF 162
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
Specific Factor 1 Variant
Length = 112
Score = 28.1 bits (61), Expect = 7.0, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 27 SAFGFVHKITTFEKTAGFQALVQFSDTETASSAKNALDGR 66
S FG + K+ F++ A V F D E A LDGR
Sbjct: 48 SKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGR 87
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 28.1 bits (61), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 109 LPVAPSAIDASG--QLSVGLDGKKLEPES-NVLLASIENMQYAVTLDVLHMVFSAFGP-- 163
LP ++ DASG Q V L +LE L ASI N+Q +L + + SA GP
Sbjct: 166 LPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAI 225
Query: 164 --VQKIAMFDKNGGLQALIQYPDV 185
+ 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
0.318 0.132 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,812,561
Number of Sequences: 62578
Number of extensions: 323745
Number of successful extensions: 588
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 565
Number of HSP's gapped (non-prelim): 27
length of query: 340
length of database: 14,973,337
effective HSP length: 99
effective length of query: 241
effective length of database: 8,778,115
effective search space: 2115525715
effective search space used: 2115525715
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: 52 (24.6 bits)