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= 026793
(233 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 97.4 bits (241), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 58/126 (46%), Positives = 77/126 (61%), Gaps = 9/126 (7%)
Query: 15 ESNVLLASIENMQYAVTVDVLNTVFSAFGTVQKVAIFEKNGGTQALIQYPDITTAAVAKE 74
+S VL +EN+ Y VT+DVL+ +FS FGTV K+ F KN QAL+QY D +A AK
Sbjct: 30 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKL 89
Query: 75 SLEGHCIYDGGYCKLHLSYSRHTDLNVKAYSDKSRDYTVQDQTLLATQQIPSVPAAPSVW 134
SL+G IY+ C L + +S+ T LNVK +DKSRDYT D +PS + PS+
Sbjct: 90 SLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPD--------LPSGDSQPSLD 140
Query: 135 QSHQAA 140
Q+ AA
Sbjct: 141 QTMAAA 146
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 97.4 bits (241), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 58/126 (46%), Positives = 77/126 (61%), Gaps = 9/126 (7%)
Query: 15 ESNVLLASIENMQYAVTVDVLNTVFSAFGTVQKVAIFEKNGGTQALIQYPDITTAAVAKE 74
+S VL +EN+ Y VT+DVL+ +FS FGTV K+ F KN QAL+QY D +A AK
Sbjct: 43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKL 102
Query: 75 SLEGHCIYDGGYCKLHLSYSRHTDLNVKAYSDKSRDYTVQDQTLLATQQIPSVPAAPSVW 134
SL+G IY+ C L + +S+ T LNVK +DKSRDYT D +PS + PS+
Sbjct: 103 SLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPD--------LPSGDSQPSLD 153
Query: 135 QSHQAA 140
Q+ AA
Sbjct: 154 QTMAAA 159
>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 = 93.6 bits (231), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 49/95 (51%), Positives = 63/95 (66%), Gaps = 1/95 (1%)
Query: 18 VLLASIENMQYAVTVDVLNTVFSAFGTVQKVAIFEKNGGTQALIQYPDITTAAVAKESLE 77
VL +EN+ Y VT+DVL+ +FS FGTV K+ F KN QAL+QY D +A AK SL+
Sbjct: 28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLD 87
Query: 78 GHCIYDGGYCKLHLSYSRHTDLNVKAYSDKSRDYT 112
G IY+ C L + +S+ T LNVK +DKSRDYT
Sbjct: 88 GQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYT 121
>pdb|2E5I|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Heterogeneous Nuclear Ribonucleoprotein L-Like
Length = 124
Score = 77.0 bits (188), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 43/97 (44%), Positives = 60/97 (61%), Gaps = 2/97 (2%)
Query: 16 SNVLLASIENMQYAVTVDVLNTVFSAFGTVQKVAIFEKNGGTQALIQYPDITTAAVAKES 75
+ VLL SI+N Y +TVDVL TV + G VQ++ IF++N G QA++++ + A AK +
Sbjct: 23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-GIQAMVEFESVLCAQKAKAA 81
Query: 76 LEGHCIYDGGYCKLHLSYSRHTDLNVKAYSDKSRDYT 112
L G IY G C L + Y+R T LNV + S DYT
Sbjct: 82 LNGADIY-AGCCTLKIEYARPTRLNVIRNDNDSWDYT 117
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 31.2 bits (69), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 23 IENMQYAVTVDVLNTVFSAFGTVQKVAIFEKNGGTQAL-------IQYPDITTAAVAKES 75
I+N+ ++ T + L VFS G ++ I +K L ++Y A A +
Sbjct: 10 IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 69
Query: 76 LEGHCIYDGGYCKLHLS 92
L+GH + DG ++ +S
Sbjct: 70 LQGHTV-DGHKLEVRIS 85
>pdb|2CVJ|A Chain A, Crystal Structure Of Thioredoxin Reductase-Related Protein
Ttha0370 From Thermus Thermophilus Hb8
pdb|2YWL|A Chain A, Crystal Structure Of Thioredoxin Reductase-Related Protein
Ttha0370 From Thermus Thermophilus Hb8
pdb|2YWL|B Chain B, Crystal Structure Of Thioredoxin Reductase-Related Protein
Ttha0370 From Thermus Thermophilus Hb8
Length = 180
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 9/73 (12%)
Query: 37 TVFSAFGTVQKVAIFEKNGGTQALIQYPDITTAAVAKESLEGHCIY---DGGYCKLHLSY 93
T+ S G ++ A + + G + YP + A VA+ + GH I DG Y +HL
Sbjct: 111 TLPSLLGLTRRGAYIDTDEGGRT--SYPRVYAAGVARGKVPGHAIISAGDGAYVAVHLV- 167
Query: 94 SRHTDLNVKAYSD 106
+DL + Y D
Sbjct: 168 ---SDLRGEPYKD 177
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 26.9 bits (58), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 30/128 (23%), Positives = 51/128 (39%), Gaps = 27/128 (21%)
Query: 23 IENMQYAVTVDVLNTVFSAFGTVQKVAIF-EKNGG--TQALIQYPDITTAAVAKESLEGH 79
+ N+ A+T D+L F G + + I +KN A ++Y A +A ++L G
Sbjct: 5 VGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGK 64
Query: 80 CIYDGGYCKLHLSYSRHT------------DLNVKAYSDKSRDYTVQDQTLL-ATQQIPS 126
I + K++ ++ DLNV V D+TL A + PS
Sbjct: 65 QI-ENNIVKINWAFQSQQSSSDDTFNLFVGDLNV----------NVDDETLRNAFKDFPS 113
Query: 127 VPAAPSVW 134
+ +W
Sbjct: 114 YLSGHVMW 121
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
0.312 0.128 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,683,592
Number of Sequences: 62578
Number of extensions: 311138
Number of successful extensions: 642
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 629
Number of HSP's gapped (non-prelim): 17
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)