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= 002966
(862 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3QZM|A Chain A, Staphylococcus Aureus Isda Neat Domain H83a Variant In
Complex With Heme
pdb|3QZM|B Chain B, Staphylococcus Aureus Isda Neat Domain H83a Variant In
Complex With Heme
Length = 127
Score = 33.5 bits (75), Expect = 0.48, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 29/61 (47%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S +SQAT + I+ Q+ G+S +A D Q P NN + Q L AS +E
Sbjct: 1 GSHMSQATSQPINFQVQKDGSSEKSAMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|1EH1|A Chain A, Ribosome Recycling Factor From Thermus Thermophilus
pdb|2V46|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 1 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 1.
pdb|2V48|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 3 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 2.
pdb|2QBE|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
First 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBG|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBI|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The First 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBK|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The Second 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4L|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The First 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|2Z4N|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The Second 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|3J0D|J Chain J, Models For The T. Thermophilus Ribosome Recycling Factor
Bound To The E. Coli Post-Termination Complex
pdb|3J0E|G Chain G, Models For The T. Thermophilus Ribosome Recycling Factor
And The E. Coli Elongation Factor G Bound To The E. Coli
Post-Termination Complex
Length = 185
Score = 33.1 bits (74), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 48/117 (41%), Gaps = 10/117 (8%)
Query: 309 NMKRMHEILERKTGGLVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATD 368
+M++ E+LE GL R+ A+ L+ V Y V LN+ P + V Q+ D
Sbjct: 13 HMQKSLEVLEHNLAGLRTGRANPALLLHLKVEYYGAHVPLNQIATVTAPDPRTLVVQSWD 72
Query: 369 KQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETDFVREVK 425
+ N+L A + N A +N+ +EE+ D VR V+
Sbjct: 73 Q----------NALKAIEKAIRDSDLGLNPSNKGDALYINIPPLTEERRKDLVRAVR 119
>pdb|1RQ8|A Chain A, Solution Structure Of The Hypothetical Protein Sav1595
From Staphylococcus Aureus, A Putative Rna Binding
Protein
Length = 104
Score = 32.7 bits (73), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 4/88 (4%)
Query: 692 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKI 751
+T +++ R L + +G+ G+ + ++ + + REL+K+ V FD K++
Sbjct: 2 LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61
Query: 752 ALALEAESGGVLVSVDKISKGYAMVVYR 779
A L + LV V G +V+YR
Sbjct: 62 AETLSEATRSELVQV----IGSMIVIYR 85
>pdb|2O1A|A Chain A, Crystal Structure Of Iron-regulated Surface Determinant
Protein A From Staphylococcus Aureus- Targeted Domain
47...188
Length = 142
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 29/61 (47%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
++ VSQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 12 STQVSQATSQPINFQVQKDGSSEKSHXDDYXQHPGKVIKQNNKYYFQTVLNNASFWKEYK 71
Query: 420 F 420
F
Sbjct: 72 F 72
>pdb|3QZL|A Chain A, Staphylococcus Aureus Isda Neat Domain K75a Variant In
Complex With Heme
Length = 127
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 28/61 (45%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S +SQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 1 GSHMSQATSQPINFQVQADGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|3QZN|A Chain A, Staphylococcus Aureus Isda Neat Domain Y166a Variant In
Complex With Heme
pdb|3QZN|B Chain B, Staphylococcus Aureus Isda Neat Domain Y166a Variant In
Complex With Heme
pdb|3QZN|C Chain C, Staphylococcus Aureus Isda Neat Domain Y166a Variant In
Complex With Heme
Length = 127
Score = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 28/61 (45%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S +SQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 1 GSHMSQATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|3QZO|A Chain A, Staphylococcus Aureus Isda Neat Domain In Complex With
Heme, Reduced Crystal
pdb|3QZO|B Chain B, Staphylococcus Aureus Isda Neat Domain In Complex With
Heme, Reduced Crystal
pdb|3QZO|C Chain C, Staphylococcus Aureus Isda Neat Domain In Complex With
Heme, Reduced Crystal
pdb|3QZO|D Chain D, Staphylococcus Aureus Isda Neat Domain In Complex With
Heme, Reduced Crystal
pdb|3QZP|A Chain A, Staphylococcus Aureus Isda Neat Domain In Complex With
Cobalt- Protoporphyrin Ix
pdb|3QZP|B Chain B, Staphylococcus Aureus Isda Neat Domain In Complex With
Cobalt- Protoporphyrin Ix
Length = 127
Score = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 28/61 (45%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S +SQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 1 GSHMSQATSQPINFQVQKDGSSEKSHMDDYMQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|2ITE|A Chain A, Crystal Structure Of The Isda Neat Domain From
Staphylococcus Aureus
pdb|2ITE|B Chain B, Crystal Structure Of The Isda Neat Domain From
Staphylococcus Aureus
pdb|2ITF|A Chain A, Crystal Structure Isda Neat Domain From Staphylococcus
Aureus With Heme Bound
pdb|2ITF|B Chain B, Crystal Structure Isda Neat Domain From Staphylococcus
Aureus With Heme Bound
pdb|2ITF|C Chain C, Crystal Structure Isda Neat Domain From Staphylococcus
Aureus With Heme Bound
pdb|2ITF|D Chain D, Crystal Structure Isda Neat Domain From Staphylococcus
Aureus With Heme Bound
Length = 127
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 27/61 (44%)
Query: 360 ASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYNNVHATQVNLETASEEQETD 419
S SQAT + I+ Q+ G+S + D Q P NN + Q L AS +E
Sbjct: 1 GSHXSQATSQPINFQVQKDGSSEKSHXDDYXQHPGKVIKQNNKYYFQTVLNNASFWKEYK 60
Query: 420 F 420
F
Sbjct: 61 F 61
>pdb|1LN4|A Chain A, Crystal Structure Of E. Coli Yhby
Length = 104
Score = 29.6 bits (65), Expect = 7.1, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 692 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKK- 750
++ +++ + L +K +LLG G+ +G + + ++ EL+K VK+ T D+ K
Sbjct: 3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIK--VKIATEDRETKT 60
Query: 751 -IALALEAESGGVLVSVDKISKGYAMVVYR 779
I A+ E+G V V G +V+YR
Sbjct: 61 LIVEAIVRETGACNVQV----IGKTLVLYR 86
>pdb|3I79|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1)
pdb|3I7B|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Bumped Kinase Inhibitor Nm-Pp1
pdb|3N51|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Bumped Kinase Inhibitor
Rm-1-95
pdb|3SX9|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Bumped Kinase Inhibitor,
Rm-1-132
pdb|3SXF|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Bumped Kinase Inhibitor,
Rm-1-89
pdb|3T3U|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Bumped Kinase Inhibitor,
Rm-1-130
pdb|3T3V|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Bumped Kinase Inhibitor,
Rm-1-87
pdb|3UPX|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Inhibitor Uw1300
pdb|3UPZ|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Bumpless Bki Analog Uw1243
pdb|3V51|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Inhibitor Rm-1-176
pdb|3V5P|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Inhibitor Uw1288
pdb|3V5T|A Chain A, Calcium-Dependent Protein Kinase 1 From Toxoplasma Gondii
(Tgcdpk1) In Complex With Inhibitor Uw1299
Length = 484
Score = 29.6 bits (65), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 11/98 (11%)
Query: 292 WKTSEIVRLKIEGAPALNMKRMHEILERKTGG-----LVIWR--SGTAVSLYRGVSYEVP 344
W T I+ + + G P N ++IL++ G L W+ S +A L R + VP
Sbjct: 211 WSTGVILYILLSGCPPFNGANEYDILKKVEKGKYTFELPQWKKVSESAKDLIRKMLTYVP 270
Query: 345 SVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGNSL 382
S+ RI R+ L + T +QI + N++
Sbjct: 271 SM----RISARDALDHEWIQTYTKEQISVDVPSLDNAI 304
>pdb|3KU2|A Chain A, Crystal Structure Of Inactivated Form Of Cdpk1 From
Toxoplasma Gondii, Tgme49.101440
Length = 507
Score = 29.3 bits (64), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 11/98 (11%)
Query: 292 WKTSEIVRLKIEGAPALNMKRMHEILERKTGG-----LVIWR--SGTAVSLYRGVSYEVP 344
W T I+ + + G P N ++IL++ G L W+ S +A L R + VP
Sbjct: 234 WSTGVILYILLSGCPPFNGANEYDILKKVEKGKYTFELPQWKKVSESAKDLIRKMLTYVP 293
Query: 345 SVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGNSL 382
S+ RI R+ L + T +QI + N++
Sbjct: 294 SM----RISARDALDHEWIQTYTKEQISVDVPSLDNAI 327
>pdb|3HX4|A Chain A, Crystal Structure Of Cdpk1 Of Toxoplasma Gondii,
Tgme49_101440, In Presence Of Calcium
Length = 508
Score = 29.3 bits (64), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 11/98 (11%)
Query: 292 WKTSEIVRLKIEGAPALNMKRMHEILERKTGG-----LVIWR--SGTAVSLYRGVSYEVP 344
W T I+ + + G P N ++IL++ G L W+ S +A L R + VP
Sbjct: 235 WSTGVILYILLSGCPPFNGANEYDILKKVEKGKYTFELPQWKKVSESAKDLIRKMLTYVP 294
Query: 345 SVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGNSL 382
S+ RI R+ L + T +QI + N++
Sbjct: 295 SM----RISARDALDHEWIQTYTKEQISVDVPSLDNAI 328
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
0.315 0.132 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,665,930
Number of Sequences: 62578
Number of extensions: 948901
Number of successful extensions: 2370
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 2353
Number of HSP's gapped (non-prelim): 39
length of query: 862
length of database: 14,973,337
effective HSP length: 107
effective length of query: 755
effective length of database: 8,277,491
effective search space: 6249505705
effective search space used: 6249505705
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)