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= 032992
(129 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 = 68.6 bits (166), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 47/139 (33%), Positives = 66/139 (47%), Gaps = 28/139 (20%)
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--ID-ETDIVLEEAIGTVIHWYPGQCWIEK------------------ 107
F NSVL KTY M +D + + VL TVI WY + ++K
Sbjct: 136 FSNSVLTKTYHMKCVDCDNEPVLLHTEATVIDWYDNKNILKKNVVKKQHNKNSREVKTVQ 195
Query: 108 ---AERSFFNFFEPLEVPT 123
SFF+FF +VP
Sbjct: 196 QTVNRDSFFHFFTSHKVPN 214
>pdb|3FS3|A Chain A, Crystal Structure Of Malaria Parasite Nucleosome Assembly
Protein (Nap)
Length = 359
Score = 65.5 bits (158), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 46/139 (33%), Positives = 65/139 (46%), Gaps = 28/139 (20%)
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--ID-ETDIVLEEAIGTVIHWYPGQCWIEK------------------ 107
F NSVL KTY M +D + + VL TVI WY + ++K
Sbjct: 170 FSNSVLTKTYHMKCVDCDNEPVLLHTEATVIDWYDNKNILKKNVVKKQHNKNSREVKTVQ 229
Query: 108 ---AERSFFNFFEPLEVPT 123
SFF+FF +VP
Sbjct: 230 QTVNRDSFFHFFTSHKVPN 248
>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 = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 46/139 (33%), Positives = 65/139 (46%), Gaps = 28/139 (20%)
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--ID-ETDIVLEEAIGTVIHWYPGQCWIEK------------------ 107
F NSVL KTY M +D + + VL TVI WY + ++K
Sbjct: 126 FSNSVLTKTYHMKCVDCDNEPVLLHTEATVIDWYDNKNILKKNVVKKQHNKNSREVKTVQ 185
Query: 108 ---AERSFFNFFEPLEVPT 123
SFF+FF +VP
Sbjct: 186 QTVNRDSFFHFFTSHKVPN 204
>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 = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 39/111 (35%), Positives = 52/111 (46%), Gaps = 13/111 (11%)
Query: 1 MVQSEDKATKE------KGVPDFWFIAMESHHELRQNIVRHDQGALKYLTDIKWCRINDS 54
+V E+KA + KG+P FW A+E+ + I D L+YL DI + D
Sbjct: 93 LVDEEEKAQNDSEEEQVKGIPSFWLTALENLPIVCDTITDRDAEVLEYLQDIGLEYLTDG 152
Query: 55 E-GFKLEFTF--GPNPYFKNSVLEKTYRMIDET----DIVLEEAIGTVIHW 98
GFKL F F NP+F N +L KTY E D + + A G I W
Sbjct: 153 RPGFKLLFRFDSSANPFFTNDILCKTYFYQKELGYSGDFIYDHAEGCEISW 203
>pdb|2AYU|A Chain A, The Structure Of Nucleosome Assembly Protein Suggests A
Mechanism For Histone Binding And Shuttling
Length = 417
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 49/156 (31%), Positives = 65/156 (41%), Gaps = 35/156 (22%)
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--GPNPYFKNSVLEKTYRMIDET----DIVLEEAIGTVIHWYPGQ----- 102
GFKL F F NP+F N +L KTY E D + + A G I W
Sbjct: 226 RPGFKLLFRFDSSANPFFTNDILCKTYFYQKELGYSGDFIYDHAEGCEISWKDNAHNVTV 285
Query: 103 ---------------CWIEKAE--RSFFNFFEPLEV 121
IEK SFFNFF+P ++
Sbjct: 286 DLEMRKQRNKTTKQVRTIEKITPIESFFNFFDPPKI 321
>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 = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 51/99 (51%), Gaps = 4/99 (4%)
Query: 14 VPDFWFIAMESHHELRQNIVRHDQGALKYLTDIKWCRIND-SEGFKLEFTFGPNPYFKNS 72
+P+FW +H ++ + D+ A+ YLT ++ D G++++F F NPYF+N
Sbjct: 78 IPNFWVTTFVNHPQVSALLGEEDEEAMHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENK 137
Query: 73 VLEKTYRMIDETDIVLEEAIGTVIHWYPGQCWIEKAERS 111
VL K + M + D + T I W G+ +++ ++
Sbjct: 138 VLSKEFHMNESGDPS---SKSTEIKWKSGKDMTKRSSQT 173
>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 = 1.1, 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 = 1.3, 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|3CF4|G Chain G, Structure Of The Codh Component Of The M. Barkeri Acds
Complex
Length = 170
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 12/74 (16%)
Query: 42 YLTDIKWCRINDSEGFKLEFTFGPNPYFKNSVLEKTYRMIDETDIVLEEAIGTVIHWYPG 101
YLTD KW ++ + + + T G ++ N VL + I +E
Sbjct: 93 YLTDPKWPGLDGNGNYDMIITIGFKKFYINQVLSAAKNFSNLKTIAIE------------ 140
Query: 102 QCWIEKAERSFFNF 115
+ +I+ A SF N
Sbjct: 141 RGYIQNATMSFGNL 154
>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 = 27.3 bits (59), Expect = 2.6, 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 = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 45 DIKWCRINDSEGFKLEFTFGPNPYF 69
D+ W I++ +G+ F GP PY
Sbjct: 278 DLGWKWIHEPKGYHANFCLGPCPYI 302
>pdb|3BK1|A Chain A, Crystal Structure Analysis Of Rnase J
pdb|3BK2|A Chain A, Crystal Structure Analysis Of The Rnase JUMP COMPLEX
Length = 562
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 68 YFKNSVLEKTYRMIDETDIVLEEAIGTVIH 97
YF + T+ + D + +V+ IGT++H
Sbjct: 147 YFTLDLFRXTHSIPDNSGVVIRTPIGTIVH 176
>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 = 25.8 bits (55), Expect = 7.6, 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|1E5R|A Chain A, Proline 3-Hydroxylase (Type Ii) -Apo Form
pdb|1E5R|B Chain B, Proline 3-Hydroxylase (Type Ii) -Apo Form
pdb|1E5S|A Chain A, Proline 3-Hydroxylase (Type Ii)-Iron Form
pdb|1E5S|B Chain B, Proline 3-Hydroxylase (Type Ii)-Iron Form
Length = 290
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 76 KTYRMIDETDIVLEEAIGTVIHWYPGQCWIEKAE--RSFFNFFE 117
+T+ +++++ + TVIH PG+ W A S NF E
Sbjct: 122 RTFMVLEDSPLAFHSNEDTVIHMRPGEIWFLDAATVHSAVNFSE 165
>pdb|3T3N|A Chain A, Molecular Basis For The Recognition And Cleavage Of Rna
(Uuccgu) By The Bifunctional 5'-3' ExoENDORIBONUCLEASE
RNASE J
pdb|3T3O|A Chain A, Molecular Basis For The Recognition And Cleavage Of Rna
(Cugg) By The Bifunctional 5'-3' ExoENDORIBONUCLEASE
RNASE J
Length = 562
Score = 25.4 bits (54), Expect = 7.9, Method: Composition-based stats.
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 68 YFKNSVLEKTYRMIDETDIVLEEAIGTVIH 97
YF + T+ + D + +V+ IGT++H
Sbjct: 148 YFTLDLFRMTHSIPDNSGVVIRTPIGTIVH 177
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
0.321 0.139 0.442
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,356,984
Number of Sequences: 62578
Number of extensions: 175655
Number of successful extensions: 295
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 273
Number of HSP's gapped (non-prelim): 21
length of query: 129
length of database: 14,973,337
effective HSP length: 88
effective length of query: 41
effective length of database: 9,466,473
effective search space: 388125393
effective search space used: 388125393
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)