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= psy13546
(109 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|II Chain i, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 165
Score = 173 bits (439), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 85/97 (87%), Positives = 90/97 (92%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITV 60
MPPKFDP E+K VYLRC GGEVGATS+LAPKIGPLGLSPKKVGDDIAKATGDWKGL+ITV
Sbjct: 1 MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITV 60
Query: 61 CLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKN 97
LTIQNRQA I VVPSA++LIIKALKEPPRDRKK KN
Sbjct: 61 KLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKN 97
>pdb|3IZS|J Chain J, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O5H|L Chain L, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3J16|H Chain H, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 165
Score = 158 bits (400), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 77/97 (79%), Positives = 88/97 (90%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITV 60
MPPKFDP EVK +YLR VGGEVGA+++LAPKIGPLGLSPKKVG+DIAKAT ++KG+K+TV
Sbjct: 1 MPPKFDPNEVKYLYLRAVGGEVGASAALAPKIGPLGLSPKKVGEDIAKATKEFKGIKVTV 60
Query: 61 CLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKN 97
L IQNRQAA SVVPSA+SL+I ALKEPPRDRKK KN
Sbjct: 61 QLKIQNRQAAASVVPSASSLVITALKEPPRDRKKDKN 97
>pdb|3IZR|J Chain J, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 166
Score = 152 bits (385), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 75/98 (76%), Positives = 86/98 (87%), Gaps = 1/98 (1%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATG-DWKGLKIT 59
MPPK DPT+V V++R GGEVGA SSLAPKIGPLGLSPKK+G+DIAK T DWKGL++T
Sbjct: 1 MPPKLDPTQVVDVFVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
Query: 60 VCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKN 97
V LT+QNRQA +SVVPSAA+L+IKALKEP RDRKKVKN
Sbjct: 61 VKLTVQNRQAKVSVVPSAAALVIKALKEPERDRKKVKN 98
>pdb|3JYW|K Chain K, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
pdb|3J2K|8 Chain 8, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated
Termination Complex
Length = 138
Score = 144 bits (364), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 71/91 (78%), Positives = 82/91 (90%)
Query: 7 PTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQN 66
P EVK +YLR VGGEVGA+++LAPKIGPLGLSPKKVG+DIAKAT ++KG+K+TV L IQN
Sbjct: 1 PNEVKYLYLRAVGGEVGASAALAPKIGPLGLSPKKVGEDIAKATKEFKGIKVTVQLKIQN 60
Query: 67 RQAAISVVPSAASLIIKALKEPPRDRKKVKN 97
RQAA SVVPSA+SL+I ALKEPPRDRKK KN
Sbjct: 61 RQAAASVVPSASSLVITALKEPPRDRKKDKN 91
>pdb|1WIB|A Chain A, Solution Structure Of The N-Terminal Domain From Mouse
Hypothetical Protein Bab22488
Length = 92
Score = 140 bits (353), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 69/79 (87%), Positives = 73/79 (92%)
Query: 2 PPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVC 61
PPKFDP EVK VYLRC GGEVGATS+LAPKIGPLGLSPKKVGDDIAKATGDWKGL+ITV
Sbjct: 8 PPKFDPNEVKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVK 67
Query: 62 LTIQNRQAAISVVPSAASL 80
LTIQNRQA I VVPSA++L
Sbjct: 68 LTIQNRQAQIEVVPSASAL 86
>pdb|1S1I|K Chain K, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex
From Yeast Obtained By Docking Atomic Models For Rna
And Protein Components Into A 11.7 A Cryo-Em Map. This
File, 1s1i, Contains 60s Subunit. The 40s Ribosomal
Subunit Is In File 1s1h
Length = 131
Score = 137 bits (346), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 67/85 (78%), Positives = 78/85 (91%)
Query: 13 VYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQAAIS 72
+YLR VGGEVGA+++LAPKIGPLGLSPKKVG+DIAKAT ++KG+K+TV L IQNRQAA S
Sbjct: 1 LYLRAVGGEVGASAALAPKIGPLGLSPKKVGEDIAKATKEFKGIKVTVQLKIQNRQAAAS 60
Query: 73 VVPSAASLIIKALKEPPRDRKKVKN 97
VVPSA+SL+I ALKEPPRDRKK KN
Sbjct: 61 VVPSASSLVITALKEPPRDRKKDKN 85
>pdb|3ZF7|M Chain M, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 164
Score = 134 bits (337), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 65/97 (67%), Positives = 79/97 (81%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITV 60
MPPKFDP + V +R VGGEV AT+SLAPK+GPLGL+ KK+G+DIAK+T DWKGLK+T
Sbjct: 1 MPPKFDPNQEITVVVRAVGGEVPATASLAPKVGPLGLNAKKIGEDIAKSTKDWKGLKVTC 60
Query: 61 CLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKN 97
L ++NR A + V PS AS +I+ALKEPPRDRKKVKN
Sbjct: 61 QLRVKNRVATVVVTPSVASRLIRALKEPPRDRKKVKN 97
>pdb|3J21|H Chain H, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 164
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 46/82 (56%), Gaps = 5/82 (6%)
Query: 7 PTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQ- 65
P +V +V + GG+ L P IGPLGL+ K+V D I +AT D+ G+++ V + +
Sbjct: 2 PKQVVEVLVE--GGKATPGPPLGPAIGPLGLNVKQVVDKINEATKDFAGMQVPVKIIVDP 59
Query: 66 -NRQAAISV-VPSAASLIIKAL 85
+Q I V VP + LI K L
Sbjct: 60 VTKQFEIEVGVPPTSQLIKKEL 81
>pdb|2GNO|A Chain A, Crystal Structure Of A Dna Polymerase Iii, Gamma
Subunit-Related Protein (Tm0771) From Thermotoga
Maritima Msb8 At 2.00 A Resolution
Length = 305
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 76 SAASLIIKALKEPPRDRKKVKNDWSWHML 104
AA+ +KAL+EPP V N WH L
Sbjct: 97 QAANAFLKALEEPPEYAVIVLNTRRWHYL 125
>pdb|3E7G|A Chain A, Structure Of Human Inosox With Inhibitor Ar-C95791
pdb|3E7G|B Chain B, Structure Of Human Inosox With Inhibitor Ar-C95791
pdb|3E7G|C Chain C, Structure Of Human Inosox With Inhibitor Ar-C95791
pdb|3E7G|D Chain D, Structure Of Human Inosox With Inhibitor Ar-C95791
Length = 424
Score = 26.2 bits (56), Expect = 4.8, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 40 KKVGDDIAKATGDWKG-----LKITVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKK 94
+++G + K WK + I V + Q + I SAA +K ++ R R
Sbjct: 316 RRMGLETHKLASLWKDQAVVEINIAVLHSFQKQNVTIMDHHSAAESFMKYMQNEYRSRGG 375
Query: 95 VKNDWSWHMLP 105
DW W + P
Sbjct: 376 CPADWIWLVPP 386
>pdb|1NSI|A Chain A, Human Inducible Nitric Oxide Synthase, Zn-Bound, L-Arg
Complex
pdb|1NSI|B Chain B, Human Inducible Nitric Oxide Synthase, Zn-Bound, L-Arg
Complex
pdb|1NSI|C Chain C, Human Inducible Nitric Oxide Synthase, Zn-Bound, L-Arg
Complex
pdb|1NSI|D Chain D, Human Inducible Nitric Oxide Synthase, Zn-Bound, L-Arg
Complex
pdb|2NSI|A Chain A, Human Inducible Nitric Oxide Synthase, Zn-free, Seitu
Complex
pdb|2NSI|B Chain B, Human Inducible Nitric Oxide Synthase, Zn-free, Seitu
Complex
pdb|2NSI|C Chain C, Human Inducible Nitric Oxide Synthase, Zn-free, Seitu
Complex
pdb|2NSI|D Chain D, Human Inducible Nitric Oxide Synthase, Zn-free, Seitu
Complex
Length = 431
Score = 26.2 bits (56), Expect = 4.8, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 40 KKVGDDIAKATGDWKG-----LKITVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKK 94
+++G + K WK + I V + Q + I SAA +K ++ R R
Sbjct: 324 RRMGLETHKLASLWKDQAVVEINIAVLHSFQKQNVTIMDHHSAAESFMKYMQNEYRSRGG 383
Query: 95 VKNDWSWHMLP 105
DW W + P
Sbjct: 384 CPADWIWLVPP 394
>pdb|3EJ8|A Chain A, Structure Of Double Mutant Of Human Inos Oxygenase Domain
With Bound Immidazole
pdb|3EJ8|B Chain B, Structure Of Double Mutant Of Human Inos Oxygenase Domain
With Bound Immidazole
pdb|3EJ8|C Chain C, Structure Of Double Mutant Of Human Inos Oxygenase Domain
With Bound Immidazole
pdb|3EJ8|D Chain D, Structure Of Double Mutant Of Human Inos Oxygenase Domain
With Bound Immidazole
Length = 424
Score = 26.2 bits (56), Expect = 4.9, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 40 KKVGDDIAKATGDWKG-----LKITVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKK 94
+++G + K WK + I V + Q + I SAA +K ++ R R
Sbjct: 316 RRMGLETHKLASLWKDQAVVEINIAVLHSFQKQNVTIMDHHSAAESFMKYMQNEYRSRGG 375
Query: 95 VKNDWSWHMLP 105
DW W + P
Sbjct: 376 CPADWIWLVPP 386
>pdb|4NOS|A Chain A, Human Inducible Nitric Oxide Synthase With Inhibitor
pdb|4NOS|B Chain B, Human Inducible Nitric Oxide Synthase With Inhibitor
pdb|4NOS|C Chain C, Human Inducible Nitric Oxide Synthase With Inhibitor
pdb|4NOS|D Chain D, Human Inducible Nitric Oxide Synthase With Inhibitor
Length = 427
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 40 KKVGDDIAKATGDWKG-----LKITVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKK 94
+++G + K WK + I V + Q + I SAA +K ++ R R
Sbjct: 316 RRMGLETHKLASLWKDQAVVEINIAVIHSFQKQNVTIMDHHSAAESFMKYMQNEYRSRGG 375
Query: 95 VKNDWSWHMLP 105
DW W + P
Sbjct: 376 CPADWIWLVPP 386
>pdb|2PAC|A Chain A, Solution Structure Of Fe(ii) Cytochrome C551 From
Pseudomonas Aeruginosa As Determined By Two-dimensional
1h Nmr
pdb|351C|A Chain A, Structure Of Cytochrome C551 From P. Aeruginosa Refined
At 1.6 Angstroms Resolution And Comparison Of The Two
Redox Forms
pdb|451C|A Chain A, Structure Of Cytochrome C551 From P. Aeruginosa Refined
At 1.6 Angstroms Resolution And Comparison Of The Two
Redox Forms
Length = 82
Score = 25.4 bits (54), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 8/44 (18%)
Query: 18 VGGEVGATSSLAPKI--------GPLGLSPKKVGDDIAKATGDW 53
G+ GA + LA +I GP+ + P V DD A+ W
Sbjct: 34 FAGQAGAEAELAQRIKNGSQGVWGPIPMPPNAVSDDEAQTLAKW 77
>pdb|2EXV|A Chain A, Crystal Structure Of The F7a Mutant Of The Cytochrome
C551 From Pseudomonas Aeruginosa
pdb|2EXV|C Chain C, Crystal Structure Of The F7a Mutant Of The Cytochrome
C551 From Pseudomonas Aeruginosa
Length = 82
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 8/42 (19%)
Query: 20 GEVGATSSLAPKI--------GPLGLSPKKVGDDIAKATGDW 53
G+ GA + LA +I GP+ + P V DD A+ W
Sbjct: 36 GQAGAEAELAQRIKNGSQGVWGPIPMPPNAVSDDEAQTLAKW 77
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
0.316 0.135 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,475,041
Number of Sequences: 62578
Number of extensions: 121408
Number of successful extensions: 253
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 240
Number of HSP's gapped (non-prelim): 21
length of query: 109
length of database: 14,973,337
effective HSP length: 73
effective length of query: 36
effective length of database: 10,405,143
effective search space: 374585148
effective search space used: 374585148
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: 45 (21.9 bits)