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= psy14162
(90 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 53.5 bits (127), Expect = 3e-08, Method: Composition-based stats.
Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 5/77 (6%)
Query: 15 GDVKQHEKALVRFYDNVMQGILRHVNFDIVKCVLLASPGFVKDKFFEYMFQVFTSQQAKS 74
GD ++K L +FYD+V Q I +FD +K V+LASPGFV ++Y+F + K
Sbjct: 173 GDSSAYQKGLDKFYDSVFQSINSEFDFDKLKVVILASPGFVARGLYDYIFSMAVKLDLK- 231
Query: 75 PSVQLI-SKFQYCFFHS 90
Q++ SK ++ HS
Sbjct: 232 ---QIVKSKNKFVILHS 245
>pdb|2VGM|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-Go Decay.
pdb|3IZQ|0 Chain 0, Structure Of The Dom34-Hbs1-Gdpnp Complex Bound To A
Translating Ribosome
pdb|3J16|A Chain A, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 386
Score = 36.2 bits (82), Expect = 0.005, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 16 DVKQHEKALVRFYDNVMQGILRHVNFDIVKCVLLASPGF----VKDKFFEY 62
DV + ++ +FY + + + +NFD +K ++L SPGF + DK F+Y
Sbjct: 180 DVLKFDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQY 230
>pdb|2VGN|A Chain A, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-go Decay.
pdb|2VGN|B Chain B, Structure Of Yeast Dom34 : A Protein Related To
Translation Termination Factor Erf1 And Involved In
No-go Decay
Length = 386
Score = 35.8 bits (81), Expect = 0.006, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 16 DVKQHEKALVRFYDNVMQGILRHVNFDIVKCVLLASPGF----VKDKFFEY 62
DV + ++ +FY + + +NFD +K ++L SPGF + DK F+Y
Sbjct: 180 DVLKFDEKTEKFYKAIYSAXKKDLNFDKLKTIILCSPGFYAKILXDKIFQY 230
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 28.1 bits (61), Expect = 1.3, Method: Composition-based stats.
Identities = 11/43 (25%), Positives = 27/43 (62%)
Query: 21 EKALVRFYDNVMQGILRHVNFDIVKCVLLASPGFVKDKFFEYM 63
E ++F+ +V + + + + V+ ++A PGFVK+ F++++
Sbjct: 176 ESEEMKFFHDVAKTMEEVMKRENVEKAIVAGPGFVKEDFYKFL 218
>pdb|3BA6|A Chain A, Structure Of The Ca2e1p Phosphoenzyme Intermediate Of
The Serca Ca2+-Atpase
Length = 994
Score = 26.6 bits (57), Expect = 4.3, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 6 AEDGKLMWEGDVKQHEKALVR 26
AE+GK +WE ++Q E LVR
Sbjct: 43 AEEGKSLWELVIEQFEDLLVR 63
>pdb|2DQS|A Chain A, Crystal Structure Of The Calcium Pump With Amppcp In The
Absence Of Calcium
pdb|2EAR|A Chain A, P21 Crystal Of The Sr Ca2+-Atpase With Bound Tg
pdb|2EAT|A Chain A, Crystal Structure Of The Sr Ca2+-Atpase With Bound Cpa
And Tg
pdb|2ZBF|A Chain A, Calcium Pump Crystal Structure With Bound Bef3 And Tg In
The Absence Of Calcium
pdb|2ZBG|A Chain A, Calcium Pump Crystal Structure With Bound Alf4 And Tg In
The Absence Of Calcium
pdb|3AR2|A Chain A, Calcium Pump Crystal Structure With Bound Amppcp And
Ca2+
pdb|3AR3|A Chain A, Calcium Pump Crystal Structure With Bound Adp And Tg
pdb|3AR4|A Chain A, Calcium Pump Crystal Structure With Bound Atp And Tg In
The Absence Of Ca2+
pdb|3AR5|A Chain A, Calcium Pump Crystal Structure With Bound Tnp-Amp And Tg
pdb|3AR6|A Chain A, Calcium Pump Crystal Structure With Bound Tnp-Adp And Tg
In The Absence Of Calcium
pdb|3AR7|A Chain A, Calcium Pump Crystal Structure With Bound Tnp-Atp And Tg
In The Absence Of Ca2+
pdb|3AR8|A Chain A, Calcium Pump Crystal Structure With Bound Alf4, Tnp-Amp
And Tg
pdb|3AR9|A Chain A, Calcium Pump Crystal Structure With Bound Bef3, Tnp-Amp
And Tg In The Absence Of Calcium
pdb|2ZBE|A Chain A, Calcium Pump Crystal Structure With Bound Bef3 In The
Absence Of Calcium And Tg
pdb|2ZBE|B Chain B, Calcium Pump Crystal Structure With Bound Bef3 In The
Absence Of Calcium And Tg
pdb|2ZBD|A Chain A, Crystal Structure Of The Sr Calcium Pump With Bound
Aluminium Fluoride, Adp And Calcium
Length = 995
Score = 26.6 bits (57), Expect = 4.3, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 6 AEDGKLMWEGDVKQHEKALVR 26
AE+GK +WE ++Q E LVR
Sbjct: 44 AEEGKSLWELVIEQFEDLLVR 64
>pdb|1KJU|A Chain A, Ca2+-Atpase In The E2 State
pdb|1IWO|A Chain A, Crystal Structure Of The Sr Ca2+-Atpase In The Absence
Of Ca2+
pdb|1IWO|B Chain B, Crystal Structure Of The Sr Ca2+-Atpase In The Absence
Of Ca2+
pdb|1SU4|A Chain A, Crystal Structure Of Calcium Atpase With Two Bound
Calcium Ions
pdb|1T5S|A Chain A, Structure Of The (sr)ca2+-atpase Ca2-e1-amppcp Form
pdb|1T5T|A Chain A, Structure Of The (Sr)ca2+-Atpase Ca2-E1-Adp:alf4- Form
pdb|1VFP|A Chain A, Crystal Structure Of The Sr Ca2+-Atpase With Bound
Amppcp
pdb|1VFP|B Chain B, Crystal Structure Of The Sr Ca2+-Atpase With Bound
Amppcp
pdb|1WPG|A Chain A, Crystal Structure Of The Sr Ca2+-Atpase With Mgf4
pdb|1WPG|B Chain B, Crystal Structure Of The Sr Ca2+-Atpase With Mgf4
pdb|1WPG|C Chain C, Crystal Structure Of The Sr Ca2+-Atpase With Mgf4
pdb|1WPG|D Chain D, Crystal Structure Of The Sr Ca2+-Atpase With Mgf4
pdb|1XP5|A Chain A, Structure Of The (Sr)ca2+-Atpase E2-Alf4- Form
pdb|2AGV|A Chain A, Crystal Structure Of The Sr Ca2+-atpase With Bhq And Tg
pdb|2AGV|B Chain B, Crystal Structure Of The Sr Ca2+-atpase With Bhq And Tg
pdb|2BY4|A Chain A, Sr Ca(2+)-Atpase In The Hne2 State Complexed With The
Thapsigargin Derivative Boc-12adt.
pdb|2C88|A Chain A, Crystal Structure Of (Sr) Calcium-Atpase E2(Tg):amppcp
Form
pdb|2C8K|A Chain A, Crystal Structure Of (Sr) Calcium-Atpase E2(Tg) With
Partially Occupied Amppcp Site
pdb|2C8L|A Chain A, Crystal Structure Of (Sr) Calcium-Atpase E2(Tg) Form
pdb|2C9M|A Chain A, Structure Of (Sr) Calcium-Atpase In The Ca2e1 State
Solved In A P1 Crystal Form.
pdb|2C9M|B Chain B, Structure Of (Sr) Calcium-Atpase In The Ca2e1 State
Solved In A P1 Crystal Form.
pdb|2O9J|A Chain A, Crystal Structure Of Calcium Atpase With Bound Magnesium
Fluoride And Cyclopiazonic Acid
pdb|2OA0|A Chain A, Crystal Structure Of Calcium Atpase With Bound Adp And
Cyclopiazonic Acid
pdb|3B9B|A Chain A, Structure Of The E2 Beryllium Fluoride Complex Of The
Serca Ca2+-Atpase
pdb|3B9R|A Chain A, Serca Ca2+-Atpase E2 Aluminium Fluoride Complex Without
Thapsigargin
pdb|3B9R|B Chain B, Serca Ca2+-Atpase E2 Aluminium Fluoride Complex Without
Thapsigargin
pdb|2EAS|A Chain A, Crystal Structure Of The Sr Ca2+-Atpase With Bound Cpa
pdb|2EAU|A Chain A, Crystal Structure Of The Sr Ca2+-Atpase With Bound Cpa
In The Presence Of Curcumin
pdb|3FGO|A Chain A, Crystal Structure Of The E2 Magnesium Fluoride Complex
Of The (Sr) Ca2+-Atpase With Bound Cpa And Amppcp
pdb|3FGO|B Chain B, Crystal Structure Of The E2 Magnesium Fluoride Complex
Of The (Sr) Ca2+-Atpase With Bound Cpa And Amppcp
pdb|3FPB|A Chain A, The Structure Of Sarcoplasmic Reticulum Ca2+-Atpase
Bound To Cyclopiazonic Acid With Atp
pdb|3FPS|A Chain A, The Structure Of Sarcoplasmic Reticulum Ca2+-Atpase
Bound To Cyclopiazonic And Adp
pdb|3NAL|A Chain A, Sr Ca(2+)-Atpase In The Hne2 State Complexed With The
Thapsigargin Derivative Dtb
pdb|3NAM|A Chain A, Sr Ca(2+)-Atpase In The Hne2 State Complexed With The
Thapsigargin Derivative Dotg
pdb|3NAN|A Chain A, Sr Ca(2+)-Atpase In The Hne2 State Complexed With A
Thapsigargin Derivative Boc-(Phi)tg
pdb|3N5K|A Chain A, Structure Of The (sr)ca2+-atpase E2-alf4- Form
pdb|3N5K|B Chain B, Structure Of The (sr)ca2+-atpase E2-alf4- Form
pdb|3N8G|A Chain A, Structure Of The (sr)ca2+-atpase Ca2-e1-caamppcp Form
pdb|2YFY|A Chain A, Serca In The Hne2 State Complexed With Debutanoyl
Thapsigargin
Length = 994
Score = 26.6 bits (57), Expect = 4.3, Method: Composition-based stats.
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 6 AEDGKLMWEGDVKQHEKALVR 26
AE+GK +WE ++Q E LVR
Sbjct: 43 AEEGKSLWELVIEQFEDLLVR 63
>pdb|2VOY|B Chain B, Cryoem Model Of Copa, The Copper Transporting Atpase
From Archaeoglobus Fulgidus
Length = 42
Score = 25.4 bits (54), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 6 AEDGKLMWEGDVKQHEKALVRF 27
AE+GK +WE ++Q E LVR
Sbjct: 8 AEEGKSLWELVIEQFEDLLVRI 29
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
0.329 0.141 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,638,119
Number of Sequences: 62578
Number of extensions: 88145
Number of successful extensions: 198
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 190
Number of HSP's gapped (non-prelim): 10
length of query: 90
length of database: 14,973,337
effective HSP length: 57
effective length of query: 33
effective length of database: 11,406,391
effective search space: 376410903
effective search space used: 376410903
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)