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= 034480
(93 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HFD|A Chain A, Nucleosome Assembly Protein 1 From Plasmodium Knowlesi
Length = 276
Score = 62.0 bits (149), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 31/72 (43%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 13 GVPDFWFIAMESHHELRQNIVRHDQGALKYLTDIKWCRINDS----EGFKLEFTFGPNPY 68
+P+FW A+ +++ + I HD+ L YL DI+ I + EGF L F F PNP+
Sbjct: 76 NLPEFWLRALRNNNTVSHVIEDHDEEILVYLNDIRCDYIKKNKEKKEGFILSFHFAPNPF 135
Query: 69 FKNSVLEKTYRM 80
F NSVL KTY M
Sbjct: 136 FSNSVLTKTYHM 147
>pdb|3FS3|A Chain A, Crystal Structure Of Malaria Parasite Nucleosome Assembly
Protein (Nap)
Length = 359
Score = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 13 GVPDFWFIAMESHHELRQNIVRHDQGALKYLTDIKWCRINDS----EGFKLEFTFGPNPY 68
+P+FW A+ +++ + I HD+ L YL DI+ I + EGF L F F NP+
Sbjct: 110 NLPEFWLRALRNNNTVSHVIEDHDEEILVYLNDIRCDYIKKNKEKKEGFILSFYFATNPF 169
Query: 69 FKNSVLEKTYRM 80
F NSVL KTY M
Sbjct: 170 FSNSVLTKTYHM 181
>pdb|3GYV|A Chain A, Crystal Structure Of Nucleosome Assembly Protein From
Plasmodium Falciparum
pdb|3GYW|A Chain A, Crystal Structure Of Nucleosome Assembly Protein From
Plasmodium Falciparum At 2.4 A Resolution
Length = 249
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 13 GVPDFWFIAMESHHELRQNIVRHDQGALKYLTDIKWCRINDS----EGFKLEFTFGPNPY 68
+P+FW A+ +++ + I HD+ L YL DI+ I + EGF L F F NP+
Sbjct: 66 NLPEFWLRALRNNNTVSHVIEDHDEEILVYLNDIRCDYIKKNKEKKEGFILSFYFATNPF 125
Query: 69 FKNSVLEKTYRM 80
F NSVL KTY M
Sbjct: 126 FSNSVLTKTYHM 137
>pdb|2Z2R|A Chain A, Nucleosome Assembly Proteins I (Nap-1, 74-365)
pdb|2Z2R|B Chain B, Nucleosome Assembly Proteins I (Nap-1, 74-365)
Length = 292
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 2 VQSEDKATKEKGVPDFWFIAMESHHELRQNIVRHDQGALKYLTDIKWCRINDSE-GFKLE 60
Q++ + + KG+P FW A+E+ + I D L+YL DI + D GFKL
Sbjct: 100 AQNDSEEEQVKGIPSFWLTALENLPIVCDTITDRDAEVLEYLQDIGLEYLTDGRPGFKLL 159
Query: 61 FTF--GPNPYFKNSVLEKTY 78
F F NP+F N +L KTY
Sbjct: 160 FRFDSSANPFFTNDILCKTY 179
>pdb|2AYU|A Chain A, The Structure Of Nucleosome Assembly Protein Suggests A
Mechanism For Histone Binding And Shuttling
Length = 417
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 33/87 (37%), Positives = 44/87 (50%), Gaps = 9/87 (10%)
Query: 1 MVQSEDKATKE------KGVPDFWFIAMESHHELRQNIVRHDQGALKYLTDIKWCRINDS 54
+V E+KA + KG+P FW A+E+ + I D L+YL DI + D
Sbjct: 166 LVDEEEKAQNDSEEEQVKGIPSFWLTALENLPIVCDTITDRDAEVLEYLQDIGLEYLTDG 225
Query: 55 E-GFKLEFTF--GPNPYFKNSVLEKTY 78
GFKL F F NP+F N +L KTY
Sbjct: 226 RPGFKLLFRFDSSANPFFTNDILCKTY 252
>pdb|2E50|A Chain A, Crystal Structure Of SetTAF-1betaINHAT
pdb|2E50|B Chain B, Crystal Structure Of SetTAF-1betaINHAT
pdb|2E50|P Chain P, Crystal Structure Of SetTAF-1betaINHAT
pdb|2E50|Q Chain Q, Crystal Structure Of SetTAF-1betaINHAT
Length = 225
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 14 VPDFWFIAMESHHELRQNIVRHDQGALKYLTDIKWCRIND-SEGFKLEFTFGPNPYFKNS 72
+P+FW +H ++ + D+ A+ YLT ++ D G++++F F NPYF+N
Sbjct: 78 IPNFWVTTFVNHPQVSALLGEEDEEAMHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENK 137
Query: 73 VLEKTYRMIDETD 85
VL K + M + D
Sbjct: 138 VLSKEFHMNESGD 150
>pdb|2Y6P|A Chain A, Evidence For A Two-Metal-Ion-Mechanism In The
Kdo-Cytidylyltransferase Kdsb
pdb|2Y6P|B Chain B, Evidence For A Two-Metal-Ion-Mechanism In The
Kdo-Cytidylyltransferase Kdsb
pdb|2Y6P|C Chain C, Evidence For A Two-Metal-Ion-Mechanism In The
Kdo-Cytidylyltransferase Kdsb
Length = 234
Score = 28.5 bits (62), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 31 NIVRHDQGALKYLTDIKWCRINDSEGFKLEFTFGPNPYFKNS 72
+ R D+ A + D+K + D EG+ L F+ P PYF+ +
Sbjct: 119 TLARKDKEAYERPEDVKV--VLDREGYALYFSRSPIPYFRKN 158
>pdb|3J21|S Chain S, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 155
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 20 IAMESHHELRQNIVRHDQGALKYLTDI-------KWCRINDSEGFKLEFTFGPNPY 68
+A+E ELR ++ AL+YL D+ R NDS+G K FGP Y
Sbjct: 31 LAVEVCRELRGMML---NDALRYLDDVIALKRPVPLKRYNDSQGHKPGKGFGPGRY 83
>pdb|1VYH|C Chain C, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|D Chain D, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|G Chain G, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|H Chain H, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|K Chain K, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|L Chain L, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|O Chain O, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|P Chain P, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|S Chain S, Paf-Ah Holoenzyme: Lis1ALFA2
pdb|1VYH|T Chain T, Paf-Ah Holoenzyme: Lis1ALFA2
Length = 410
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 4/78 (5%)
Query: 18 WFIAM-ESHHELRQNIVRHDQGALKYLTDIKWCRINDSEGFKLEFTFGPNPYFKNSVLEK 76
W +A E ELR++ RH + + + + I+++ G + + + P P+ + +K
Sbjct: 261 WVVATKECKAELREH--RHVVECISWAPESSYSSISEATGSETKKSGKPGPFLLSGSRDK 318
Query: 77 TYRMID-ETDIVLEEAIG 93
T +M D T + L +G
Sbjct: 319 TIKMWDVSTGMCLMTLVG 336
>pdb|3RJR|A Chain A, Crystal Structure Of Pro-tgf Beta 1
pdb|3RJR|B Chain B, Crystal Structure Of Pro-tgf Beta 1
pdb|3RJR|C Chain C, Crystal Structure Of Pro-tgf Beta 1
pdb|3RJR|D Chain D, Crystal Structure Of Pro-tgf Beta 1
Length = 363
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 40 LKYLTDIKWCRINDSEGFKLEFTFGPNPY 68
+ + D+ W I++ +G+ F GP PY
Sbjct: 273 IDFRKDLGWKWIHEPKGYHANFCLGPCPY 301
>pdb|1KLD|A Chain A, Solution Structure Of Tgf-B1, Nmr, Models 18-33 Of 33
Structures
pdb|1KLD|B Chain B, Solution Structure Of Tgf-B1, Nmr, Models 18-33 Of 33
Structures
pdb|1KLC|A Chain A, Solution Structure Of Tgf-B1, Nmr, Minimized Average
Structure
pdb|1KLC|B Chain B, Solution Structure Of Tgf-B1, Nmr, Minimized Average
Structure
pdb|1KLA|A Chain A, Solution Structure Of Tgf-B1, Nmr, Models 1-17 Of 33
Structures
pdb|1KLA|B Chain B, Solution Structure Of Tgf-B1, Nmr, Models 1-17 Of 33
Structures
pdb|3KFD|A Chain A, Ternary Complex Of Tgf-B1 Reveals Isoform-Specific
Ligand Re And Receptor Recruitment In The Superfamily
pdb|3KFD|B Chain B, Ternary Complex Of Tgf-B1 Reveals Isoform-Specific
Ligand Re And Receptor Recruitment In The Superfamily
pdb|3KFD|C Chain C, Ternary Complex Of Tgf-B1 Reveals Isoform-Specific
Ligand Re And Receptor Recruitment In The Superfamily
pdb|3KFD|D Chain D, Ternary Complex Of Tgf-B1 Reveals Isoform-Specific
Ligand Re And Receptor Recruitment In The Superfamily
Length = 112
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 45 DIKWCRINDSEGFKLEFTFGPNPYF 69
D+ W I++ +G+ F GP PY
Sbjct: 27 DLGWKWIHEPKGYHANFCLGPCPYI 51
>pdb|3CF4|G Chain G, Structure Of The Codh Component Of The M. Barkeri Acds
Complex
Length = 170
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 22/49 (44%)
Query: 42 YLTDIKWCRINDSEGFKLEFTFGPNPYFKNSVLEKTYRMIDETDIVLEE 90
YLTD KW ++ + + + T G ++ N VL + I +E
Sbjct: 93 YLTDPKWPGLDGNGNYDMIITIGFKKFYINQVLSAAKNFSNLKTIAIER 141
>pdb|1KTZ|A Chain A, Crystal Structure Of The Human Tgf-Beta Type Ii Receptor
Extracellular Domain In Complex With Tgf-Beta3
pdb|1TGJ|A Chain A, Human Transforming Growth Factor-beta 3, Crystallized
From Dioxane
pdb|1TGK|A Chain A, Human Transforming Growth Factor Beta 3, Crystallized
From Peg 4000
pdb|2PJY|A Chain A, Structural Basis For Cooperative Assembly Of The
Tgf-Beta Signaling Complex
pdb|3EO1|C Chain C, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|F Chain F, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|I Chain I, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
pdb|3EO1|L Chain L, Structure Of The Fab Fragment Of Gc-1008 In Complex With
Transforming Growth Factor-Beta 3
Length = 112
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 45 DIKWCRINDSEGFKLEFTFGPNPYFKNS 72
D+ W +++ +G+ F GP PY +++
Sbjct: 27 DLGWKWVHEPKGYYANFCSGPCPYLRSA 54
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 0.137 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,017,861
Number of Sequences: 62578
Number of extensions: 111270
Number of successful extensions: 189
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 173
Number of HSP's gapped (non-prelim): 13
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
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: 45 (21.9 bits)