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= psy5840
(132 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NLQ|A Chain A, The Crystal Structure Of Drosophila Nlp-Core Provides
Insight Into Pentamer Formation And Histone Binding
pdb|1NLQ|B Chain B, The Crystal Structure Of Drosophila Nlp-Core Provides
Insight Into Pentamer Formation And Histone Binding
pdb|1NLQ|C Chain C, The Crystal Structure Of Drosophila Nlp-Core Provides
Insight Into Pentamer Formation And Histone Binding
pdb|1NLQ|D Chain D, The Crystal Structure Of Drosophila Nlp-Core Provides
Insight Into Pentamer Formation And Histone Binding
pdb|1NLQ|E Chain E, The Crystal Structure Of Drosophila Nlp-Core Provides
Insight Into Pentamer Formation And Histone Binding
Length = 108
Score = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 48/75 (64%), Gaps = 3/75 (4%)
Query: 1 MFLFQAVIGANAKEGEVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDPPVTF 60
+ + Q ++GA AKE E +VVEV + +++PI VLKA P D+ F + VTF
Sbjct: 32 LVIKQILLGAEAKENEFNVVEVNTP--KDSVQIPIAVLKAGETRAVNP-DVEFYESKVTF 88
Query: 61 KLVKGSGPIYLFGNH 75
KL+KGSGP+Y+ G++
Sbjct: 89 KLIKGSGPVYIHGHN 103
>pdb|2VTX|A Chain A, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
pdb|2VTX|B Chain B, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
pdb|2VTX|C Chain C, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
pdb|2VTX|D Chain D, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
pdb|2VTX|E Chain E, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
pdb|2VTX|G Chain G, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
pdb|2VTX|H Chain H, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
pdb|2VTX|I Chain I, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
pdb|2VTX|K Chain K, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
Length = 120
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 1 MFLFQAVIGANAKEGEVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDPPVTF 60
+ L +G AK+ E H+VE+ A+ +PI LK + + A + + DPPVTF
Sbjct: 45 LALRTVCLGDKAKD-EFHIVEIVDQEEGAEKSVPIATLKPS-ILPMATMVGIELDPPVTF 102
Query: 61 KLVKGSGPIYLFGNH 75
+L GSGP+Y+ G H
Sbjct: 103 RLKAGSGPLYISGQH 117
>pdb|2P1B|A Chain A, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|B Chain B, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|C Chain C, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|D Chain D, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|E Chain E, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|F Chain F, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|G Chain G, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|H Chain H, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|I Chain I, Crystal Structure Of Human Nucleophosmin-Core
pdb|2P1B|J Chain J, Crystal Structure Of Human Nucleophosmin-Core
Length = 122
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 8 IGANAKEGEVHVVEVEAMGFRAD-IKLPIVVLKAAGVNNHAPLDLLFPDPPVTFKLVKGS 66
+GA AK+ E+H+VE EAM + IK+ + LK + V L PPV +L GS
Sbjct: 41 LGAGAKD-ELHIVEAEAMNYEGSPIKVTLATLKMS-VQPTVSLGGFEITPPVVLRLKCGS 98
Query: 67 GPIYLFGNHSVGTGEPM 83
GP+++ G H V E +
Sbjct: 99 GPVHISGQHLVAVEEDL 115
>pdb|2VTX|J Chain J, Activation Of Nucleoplasmin, An Oligomeric Histone
Chaperone, Challenges Its Stability
Length = 120
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 3 LFQAVIGANAKEGEVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDPPVTFKL 62
L +G AK+ E H+VE+ A+ +PI LK + + A + + DPPVTF+L
Sbjct: 47 LRTVCLGDKAKD-EFHIVEIVDQEEGAEKVVPIATLKPS-ILPMATMVGIELDPPVTFRL 104
Query: 63 VKGSGPIYLFGNH 75
GSGP+Y+ G H
Sbjct: 105 KAGSGPLYISGQH 117
>pdb|1XB9|A Chain A, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|B Chain B, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|C Chain C, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|D Chain D, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|E Chain E, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|F Chain F, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|G Chain G, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|H Chain H, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|I Chain I, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XB9|J Chain J, The Structure And Function Of Xenopus No38-Core, A Histone
Chaperone In The Nucleolus
pdb|1XE0|A Chain A, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|B Chain B, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|C Chain C, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|D Chain D, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|E Chain E, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|F Chain F, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|G Chain G, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|H Chain H, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|I Chain I, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
pdb|1XE0|J Chain J, The Structure And Function Of Xenopus No38-Core, A Histone
Binding Chaperone In The Nucleolus
Length = 114
Score = 42.4 bits (98), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 8 IGANAKEGEVHVVEVEAMGFRAD-IKLPIVVLKAAGVNNHAPLDLLFPDPPVTFKLVKGS 66
+GA+AK+ E+HVVE E + + IK+ + LK + V L PPV +L GS
Sbjct: 41 LGASAKD-ELHVVEAEGINYEGKTIKIALASLKPS-VQPTVSLGGFEITPPVILRLKSGS 98
Query: 67 GPIYLFGNHSVG 78
GP+Y+ G H V
Sbjct: 99 GPVYVSGQHLVA 110
>pdb|1K5J|A Chain A, The Crystal Structure Of Nucleoplasmin-Core
pdb|1K5J|B Chain B, The Crystal Structure Of Nucleoplasmin-Core
pdb|1K5J|C Chain C, The Crystal Structure Of Nucleoplasmin-Core
pdb|1K5J|D Chain D, The Crystal Structure Of Nucleoplasmin-Core
pdb|1K5J|E Chain E, The Crystal Structure Of Nucleoplasmin-Core
Length = 124
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 3 LFQAVIGANAKEGEVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDPPVTFKL 62
L +G AK+ E H+VE+ A+ +PI LK + + A + + PPVTF+L
Sbjct: 47 LRTVCLGDKAKD-EFHIVEIVTQEEGAEKSVPIATLKPS-ILPMATMVGIELTPPVTFRL 104
Query: 63 VKGSGPIYLFGNH 75
GSGP+Y+ G H
Sbjct: 105 KAGSGPLYISGQH 117
>pdb|3T30|B Chain B, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|E Chain E, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|D Chain D, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|A Chain A, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|C Chain C, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|H Chain H, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|I Chain I, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|J Chain J, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|F Chain F, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
pdb|3T30|G Chain G, Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes
And Early Embryos
Length = 110
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 1 MFLFQAVIGANAKEGEVHVVEVEAMGFRADIKLPIVVLKA--AGVNNHAPLDLLFPDPPV 58
+ L +G AKE E+H VE+ + D K+ V + + A V + + PPV
Sbjct: 32 LLLHTICLGEKAKE-EMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPV 90
Query: 59 TFKLVKGSGPIYLFGNH 75
TF+L GSGP++L G
Sbjct: 91 TFQLRAGSGPVFLSGQE 107
>pdb|2JOZ|A Chain A, Solution Nmr Structure Of Protein Yxef, Northeast
Structural Genomics Consortium Target Sr500a
Length = 135
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 16 EVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDP--PVTFKLVKG 65
E VVE E M R +++LP + K + +++ + P P+ L +G
Sbjct: 42 EDEVVETEVMEGRGEVQLPFMAYKVISQSTDGSIEIQYLGPYYPLKSTLKRG 93
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
0.322 0.142 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,068,767
Number of Sequences: 62578
Number of extensions: 100996
Number of successful extensions: 147
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 137
Number of HSP's gapped (non-prelim): 9
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)