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= 008445
(565 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 7/66 (10%)
Query: 352 TEDDVSNYFNTYGPVDD---VRIPCQQK-RMFGFVTFASADTVKMILAKGNPHFVCGARV 407
TE+ + NY+ +G + D +R P ++ R FGFVTF+S V +A PH + G
Sbjct: 40 TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGR-- 96
Query: 408 LVKPYR 413
+V+P R
Sbjct: 97 VVEPKR 102
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 352 TEDDVSNYFNTYGPVDDVRI----PCQQKRMFGFVTFASADTVKMI 393
T +DV +YF +G VDD + + R FGFVTF S D V+ +
Sbjct: 12 TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 56/126 (44%), Gaps = 10/126 (7%)
Query: 305 RPHGQHAVILAEDAPKYLENRNERSDPGPIVTGSRQIYLTFPAESTFTEDDVSNYFNTYG 364
RPH ++ PK +R + PG +T ++I++ E T E + +YF YG
Sbjct: 76 RPHKVDGRVVE---PKRAVSREDSQRPGAHLT-VKKIFVGGIKEDT-EEHHLRDYFEQYG 130
Query: 365 PVDDVRIPCQ----QKRMFGFVTFASADTVKMILAKGNPHFVCGARVLVKPYREKSKLVD 420
++ + I +KR F FVTF D+V I+ + H V G V+ K ++
Sbjct: 131 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMAS 189
Query: 421 RKYQER 426
+R
Sbjct: 190 ASSSQR 195
Score = 32.7 bits (73), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 352 TEDDVSNYFNTYGPVDD---VRIP-CQQKRMFGFVTFASADTVKMILAKGNPHFVCGARV 407
T++ + ++F +G + D +R P ++ R FGFVT+A+ + V + PH V G
Sbjct: 27 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGR-- 83
Query: 408 LVKPYREKSK 417
+V+P R S+
Sbjct: 84 VVEPKRAVSR 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 349 STFTEDDVSNYFNTYGPVDDVRIPC----QQKRMFGFVTFASADTVKMILAKGNPHFVCG 404
+T E + F YGP++ V+I C +Q R +GFV F S + + +A N +
Sbjct: 52 TTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN 111
Query: 405 ARVLV 409
R+ V
Sbjct: 112 KRLKV 116
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 56/126 (44%), Gaps = 10/126 (7%)
Query: 305 RPHGQHAVILAEDAPKYLENRNERSDPGPIVTGSRQIYLTFPAESTFTEDDVSNYFNTYG 364
RPH ++ PK +R + PG +T ++I++ E T E + +YF YG
Sbjct: 75 RPHKVDGRVVE---PKRAVSREDSQRPGAHLT-VKKIFVGGIKEDT-EEHHLRDYFEQYG 129
Query: 365 PVDDVRIPCQ----QKRMFGFVTFASADTVKMILAKGNPHFVCGARVLVKPYREKSKLVD 420
++ + I +KR F FVTF D+V I+ + H V G V+ K ++
Sbjct: 130 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMAS 188
Query: 421 RKYQER 426
+R
Sbjct: 189 ASSSQR 194
Score = 32.7 bits (73), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 352 TEDDVSNYFNTYGPVDD---VRIP-CQQKRMFGFVTFASADTVKMILAKGNPHFVCGARV 407
T++ + ++F +G + D +R P ++ R FGFVT+A+ + V + PH V G
Sbjct: 26 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGR-- 82
Query: 408 LVKPYREKSK 417
+V+P R S+
Sbjct: 83 VVEPKRAVSR 92
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 56/126 (44%), Gaps = 10/126 (7%)
Query: 305 RPHGQHAVILAEDAPKYLENRNERSDPGPIVTGSRQIYLTFPAESTFTEDDVSNYFNTYG 364
RPH ++ PK +R + PG +T ++I++ E T E + +YF YG
Sbjct: 74 RPHKVDGRVVE---PKRAVSREDSQRPGAHLT-VKKIFVGGIKEDT-EEHHLRDYFEQYG 128
Query: 365 PVDDVRIPCQ----QKRMFGFVTFASADTVKMILAKGNPHFVCGARVLVKPYREKSKLVD 420
++ + I +KR F FVTF D+V I+ + H V G V+ K ++
Sbjct: 129 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMAS 187
Query: 421 RKYQER 426
+R
Sbjct: 188 ASSSQR 193
Score = 32.7 bits (73), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 352 TEDDVSNYFNTYGPVDD---VRIP-CQQKRMFGFVTFASADTVKMILAKGNPHFVCGARV 407
T++ + ++F +G + D +R P ++ R FGFVT+A+ + V + PH V G
Sbjct: 25 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGR-- 81
Query: 408 LVKPYREKSK 417
+V+P R S+
Sbjct: 82 VVEPKRAVSR 91
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 54/118 (45%), Gaps = 10/118 (8%)
Query: 305 RPHGQHAVILAEDAPKYLENRNERSDPGPIVTGSRQIYLTFPAESTFTEDDVSNYFNTYG 364
RPH ++ PK +R + PG +T ++I++ E T E + +YF YG
Sbjct: 68 RPHKVDGRVVE---PKRAVSREDSQRPGAHLT-VKKIFVGGIKEDT-EEHHLRDYFEQYG 122
Query: 365 PVDDVRIPCQ----QKRMFGFVTFASADTVKMILAKGNPHFVCGARVLVKPYREKSKL 418
++ + I +KR F FVTF D+V I+ + H V G V+ K ++
Sbjct: 123 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM 179
Score = 32.3 bits (72), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 352 TEDDVSNYFNTYGPVDD---VRIP-CQQKRMFGFVTFASADTVKMILAKGNPHFVCGARV 407
T++ + ++F +G + D +R P ++ R FGFVT+A+ + V + PH V G
Sbjct: 19 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGR-- 75
Query: 408 LVKPYREKSK 417
+V+P R S+
Sbjct: 76 VVEPKRAVSR 85
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 9/94 (9%)
Query: 305 RPHGQHAVILAEDAPKYLENRNERSDPGPIVTGSRQIYLTFPAESTFTEDDVSNYFNTYG 364
RPH ++ PK +R + PG +T ++I++ E T E + +YF YG
Sbjct: 75 RPHKVDGRVVE---PKRAVSREDSQRPGAHLT-VKKIFVGGIKEDT-EEHHLRDYFEQYG 129
Query: 365 PVDDVRIPCQ----QKRMFGFVTFASADTVKMIL 394
++ + I +KR F FVTF D+V I+
Sbjct: 130 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 32.0 bits (71), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 352 TEDDVSNYFNTYGPVDD---VRIP-CQQKRMFGFVTFASADTVKMILAKGNPHFVCGARV 407
T++ + ++F +G + D +R P ++ R FGFVT+A+ + V + PH V G
Sbjct: 26 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGR-- 82
Query: 408 LVKPYREKSK 417
+V+P R S+
Sbjct: 83 VVEPKRAVSR 92
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 9/94 (9%)
Query: 305 RPHGQHAVILAEDAPKYLENRNERSDPGPIVTGSRQIYLTFPAESTFTEDDVSNYFNTYG 364
RPH ++ PK +R + PG +T ++I++ E T E + +YF YG
Sbjct: 73 RPHKVDGRVVE---PKRAVSREDSQRPGAHLT-VKKIFVGGIKEDT-EEHHLRDYFEQYG 127
Query: 365 PVDDVRIPCQ----QKRMFGFVTFASADTVKMIL 394
++ + I +KR F FVTF D+V I+
Sbjct: 128 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 32.0 bits (71), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 352 TEDDVSNYFNTYGPVDD---VRIP-CQQKRMFGFVTFASADTVKMILAKGNPHFVCGARV 407
T++ + ++F +G + D +R P ++ R FGFVT+A+ + V + PH V G
Sbjct: 24 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGR-- 80
Query: 408 LVKPYREKSK 417
+V+P R S+
Sbjct: 81 VVEPKRAVSR 90
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 35.4 bits (80), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 352 TEDDVSNYFNTYGPVDDVRI----PCQQKRMFGFVTFASADTVKMILAKGNPHFVCGARV 407
T++ + +YF+ YG V D I Q R FGFV F + V +LA PH + G +
Sbjct: 29 TQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNI 87
Query: 408 LVKP 411
KP
Sbjct: 88 DPKP 91
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.4 bits (80), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 10/59 (16%)
Query: 352 TEDDVSNYFNTYGPVDDVRIPCQQKRMFGFVTFASADTVKMILAKGNPHFVCGARVLVK 410
TED++ +F+ YG V DV IP + R F FVTFA + + CG +++K
Sbjct: 18 TEDELREFFSQYGDVMDVFIP-KPFRAFAFVTFADDQIAQSL---------CGEDLIIK 66
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 329 SDPGPIVTGSRQIYLTFPAESTFTEDDVSNYFNTYGPVDDVRI----PCQQKRMFGFVTF 384
SD G + G L+F E + F+ YG + +V + Q+ R FGFVTF
Sbjct: 10 SDEGKLFVGG----LSFDT----NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61
Query: 385 ASADTVKMILAKGNPHFVCGARVLV 409
+ D K + N V G ++ V
Sbjct: 62 ENIDDAKDAMMAMNGKSVDGRQIRV 86
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 33.1 bits (74), Expect = 0.39, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 352 TEDDVSNYFNTYGPVDDVRI----PCQQKRMFGFVTFASADTVKMIL 394
TED++ YF YG V D++I + R FGF++F +V ++
Sbjct: 16 TEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
>pdb|2CQE|A Chain A, Solution Structure Of The Zinc-Finger Domain In Kiaa1064
Protein
Length = 98
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 178 NAELPVKT--CHYFNKGFCKHGSNCRYYHGLVSESFTQMFGQTSPDGFN-DDHLFS 230
+ ELP K C ++ GFC NC Y HG F T+ + N DD +FS
Sbjct: 6 SGELPKKRELCKFYITGFCARAENCPYMHG----DFPCKLYHTTGNCINGDDCMFS 57
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 350 TFTEDDVSNYFNTYGPVDDVRIPC----QQKRMFGFVTF 384
T +E+D+ F+ YGP+ ++ P ++ + F FVTF
Sbjct: 19 TSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 9/64 (14%)
Query: 353 EDDVSNYFNTYGPVDDVRI----PCQQKRMFGFVTFASADTVKMILAKGNPHF--VCGAR 406
E ++ YF +G V +V + Q+ R FGF+TF +V + N HF + G +
Sbjct: 24 ETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV---NMHFHDIMGKK 80
Query: 407 VLVK 410
V VK
Sbjct: 81 VEVK 84
>pdb|4II1|A Chain A, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|B Chain B, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|C Chain C, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|D Chain D, Crystal Structure Of The Zinc Finger Of Zgpat
Length = 167
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 183 VKTCHYFNKGFCKHGSNCRYYHGLV 207
+K C +F +G C+ NCR+ HG V
Sbjct: 76 LKPCPFFLEGKCRFKENCRFSHGQV 100
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 29.3 bits (64), Expect = 6.3, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 338 SRQIYLTFPAESTFTEDDVSNYFNTYGPVDDVRIPCQQK----RMFGFVTFASADTVKMI 393
S I L P ++T E D+ YF+T+G V V++ K + FGFV F +T +
Sbjct: 16 SDLIVLGLPWKTT--EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 394 LAK 396
+++
Sbjct: 74 MSQ 76
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 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,050,102
Number of Sequences: 62578
Number of extensions: 634106
Number of successful extensions: 1636
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1624
Number of HSP's gapped (non-prelim): 26
length of query: 565
length of database: 14,973,337
effective HSP length: 104
effective length of query: 461
effective length of database: 8,465,225
effective search space: 3902468725
effective search space used: 3902468725
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: 54 (25.4 bits)