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= psy2899
(139 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QO1|J Chain J, Molecular Architecture Of The Rotary Motor In Atp Synthase
From Yeast Mitochondria
pdb|1AQT|A Chain A, Epsilon Subunit Of F1f0-Atp Synthase From Escherichia Coli
Length = 138
Score = 87.8 bits (216), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 49/130 (37%), Positives = 71/130 (54%), Gaps = 2/130 (1%)
Query: 2 RIDIVSIEGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXX 61
+D+VS E +FS +E I + G G+LG+YP H+PL+T IKPG
Sbjct: 5 HLDVVSAEQQMFSGL-VEKIQVTGSEGELGIYPGHAPLLTAIKPGMIRIVKQHGHEEFI- 62
Query: 62 FVSGGIIDIQPDSVIVLADTAIHGSDLVXXXXXXXXXXXXXXXYNKKSNIDYSITKAKLA 121
++SGGI+++QP +V VLADTAI G DL + ++DY+ A+LA
Sbjct: 63 YLSGGILEVQPGNVTVLADTAIRGQDLDEARAMEAKRKAEEHISSSHGDVDYAQASAELA 122
Query: 122 IIIAQLKTIQ 131
IAQL+ I+
Sbjct: 123 KAIAQLRVIE 132
>pdb|1BSH|A Chain A, Solution Structure Of The Epsilon Subunit Of The F1-
Atpsynthase From Escherichia Coli And Orientation Of The
Subunit Relative To The Beta Subunits Of The Complex
pdb|1BSN|A Chain A, Solution Structure Of The Epsilon Subunit Of The F1-
Atpsynthase From Escherichia Coli And Orientation Of The
Subunit Relative To The Beta Subunits Of The Complex
pdb|1FS0|E Chain E, Complex Of GammaEPSILON ATP SYNTHASE FROM E.COLI
pdb|3OAA|H Chain H, Structure Of The E.Coli F1-Atp Synthase Inhibited By
Subunit Epsilon
pdb|3OAA|P Chain P, Structure Of The E.Coli F1-Atp Synthase Inhibited By
Subunit Epsilon
pdb|3OAA|X Chain X, Structure Of The E.Coli F1-Atp Synthase Inhibited By
Subunit Epsilon
pdb|3OAA|FF Chain f, Structure Of The E.Coli F1-Atp Synthase Inhibited By
Subunit Epsilon
Length = 138
Score = 87.8 bits (216), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 49/130 (37%), Positives = 71/130 (54%), Gaps = 2/130 (1%)
Query: 2 RIDIVSIEGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXX 61
+D+VS E +FS +E I + G G+LG+YP H+PL+T IKPG
Sbjct: 5 HLDVVSAEQQMFSGL-VEKIQVTGSEGELGIYPGHAPLLTAIKPGMIRIVKQHGHEEFI- 62
Query: 62 FVSGGIIDIQPDSVIVLADTAIHGSDLVXXXXXXXXXXXXXXXYNKKSNIDYSITKAKLA 121
++SGGI+++QP +V VLADTAI G DL + ++DY+ A+LA
Sbjct: 63 YLSGGILEVQPGNVTVLADTAIRGQDLDEARAMEAKRKAEEHISSSHGDVDYAQASAELA 122
Query: 122 IIIAQLKTIQ 131
IAQL+ I+
Sbjct: 123 KAIAQLRVIE 132
>pdb|2E5Y|A Chain A, Epsilon Subunit And Atp Complex Of F1f0-Atp Synthase From
The Thermophilic Bacillus Ps3
pdb|2E5Y|B Chain B, Epsilon Subunit And Atp Complex Of F1f0-Atp Synthase From
The Thermophilic Bacillus Ps3
Length = 133
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/120 (21%), Positives = 57/120 (47%), Gaps = 5/120 (4%)
Query: 3 IDIVSIEGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXXF 62
+ +V+ +G ++ + ++E + + + G+LG+ P H PL+ ++
Sbjct: 6 VSVVTPDGPVYED-DVEMVSVKAKSGELGILPGHIPLVAPLE--ISAARLKKGGKTQYIA 62
Query: 63 VSGGIIDIQPDSVIVLADTAIHGSDLVXXXXXXXXXXXXXXXYNKKSNIDYSITKAKLAI 122
VSGG ++++PD V +LA A D+ +++ +ID+ +A+LA+
Sbjct: 63 VSGGFLEVRPDKVTILAQAAERAEDIDVLRAKAAKERAERRLQSQQDDIDFK--RAELAL 120
>pdb|2QE7|H Chain H, Crystal Structure Of The F1-Atpase From The
Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
Length = 135
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 44/82 (53%), Gaps = 3/82 (3%)
Query: 1 MRIDIVSIEGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXX 60
+++DIV+ E +F + + ++ G G+LGV H PL+T +K
Sbjct: 4 VQVDIVTPERKVFQGE-ADIVIARGVEGELGVMAGHIPLVTPLKTA--PVRIKQGDKETL 60
Query: 61 XFVSGGIIDIQPDSVIVLADTA 82
VSGG ++++PD V +LADTA
Sbjct: 61 IAVSGGFLEVRPDKVNILADTA 82
>pdb|2XOK|H Chain H, Refined Structure Of Yeast F1c10 Atpase Complex To 3 A
Resolution
Length = 160
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 12 LFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXXFVSGGIIDIQ 71
L+S + + LP + G +GV H P + + PG F+SGG +Q
Sbjct: 43 LYSGSEVTQVNLPAKSGRIGVLANHVPTVEQLLPGV--VEVMEGSNSKKFFISGGFATVQ 100
Query: 72 PDSVIVLADTAIHG 85
PDS + + TAI
Sbjct: 101 PDSQLCV--TAIEA 112
>pdb|2HLD|H Chain H, Crystal Structure Of Yeast Mitochondrial F1-Atpase
pdb|2HLD|Q Chain Q, Crystal Structure Of Yeast Mitochondrial F1-Atpase
pdb|2HLD|Z Chain Z, Crystal Structure Of Yeast Mitochondrial F1-Atpase
pdb|3FKS|H Chain H, Yeast F1 Atpase In The Absence Of Bound Nucleotides
pdb|3FKS|Q Chain Q, Yeast F1 Atpase In The Absence Of Bound Nucleotides
pdb|3FKS|Z Chain Z, Yeast F1 Atpase In The Absence Of Bound Nucleotides
pdb|2WPD|H Chain H, The Mg.Adp Inhibited State Of The Yeast F1c10 Atp
Synthase
pdb|3OEE|H Chain H, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Alpha-F405s
pdb|3OEE|Q Chain Q, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Alpha-F405s
pdb|3OEE|Z Chain Z, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Alpha-F405s
pdb|3OEH|H Chain H, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Beta-V279f
pdb|3OEH|Q Chain Q, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Beta-V279f
pdb|3OEH|Z Chain Z, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Beta-V279f
pdb|3OFN|H Chain H, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Alpha-N67i
pdb|3OFN|Q Chain Q, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Alpha-N67i
pdb|3ZRY|H Chain H, Rotor Architecture In The F(1)-C(10)-Ring Complex Of The
Yeast F-Atp Synthase
pdb|3ZIA|H Chain H, The Structure Of F1-atpase From Saccharomyces Cerevisiae
Inhibited By Its Regulatory Protein If1
pdb|3ZIA|R Chain R, The Structure Of F1-atpase From Saccharomyces Cerevisiae
Inhibited By Its Regulatory Protein If1
Length = 138
Score = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 12 LFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXXFVSGGIIDIQ 71
L+S + + LP + G +GV H P + + PG F+SGG +Q
Sbjct: 21 LYSGSEVTQVNLPAKSGRIGVLANHVPTVEQLLPGV--VEVMEGSNSKKFFISGGFATVQ 78
Query: 72 PDSVIVLADTAIHG 85
PDS + + TAI
Sbjct: 79 PDSQLCV--TAIEA 90
>pdb|3OE7|H Chain H, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Gamma-I270t
pdb|3OE7|Q Chain Q, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Gamma-I270t
pdb|3OE7|Z Chain Z, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
Gamma-I270t
Length = 137
Score = 35.4 bits (80), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 12 LFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXXFVSGGIIDIQ 71
L+S + + LP + G +GV H P + + PG F+SGG +Q
Sbjct: 20 LYSGSEVTQVNLPAKSGRIGVLANHVPTVEQLLPGV--VEVMEGSNSKKFFISGGFATVQ 77
Query: 72 PDSVIVLADTAIHG 85
PDS + + TAI
Sbjct: 78 PDSQLCV--TAIEA 89
>pdb|4B2Q|H Chain H, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
Subtomogram Average
pdb|4B2Q|HH Chain h, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
Subtomogram Average
Length = 132
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 12 LFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXXFVSGGIIDIQ 71
L+S + + LP + G +GV H P + + PG F+SGG +Q
Sbjct: 15 LYSGSEVTQVNLPAKSGRIGVLANHVPTVEQLLPGV--VEVMEGSNSKKFFISGGFATVQ 72
Query: 72 PDSVIVLADTAIHG 85
PDS + + TAI
Sbjct: 73 PDSQLCV--TAIEA 84
>pdb|2XND|H Chain H, Crystal Structure Of Bovine F1-C8 Sub-Complex Of Atp
Synthase
Length = 131
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 1 MRIDIVSIEGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXX 60
M S + F++ N+ + +P + G G+ H P + ++PG
Sbjct: 2 MSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRPGL-VVVHAEDGTTSK 60
Query: 61 XFVSGGIIDIQPD-SVIVLADTAI 83
FVS G + + D SV +LA+ A+
Sbjct: 61 YFVSSGSVTVNADSSVQLLAEEAV 84
>pdb|1E79|H Chain H, Bovine F1-Atpase Inhibited By Dccd
(Dicyclohexylcarbodiimide)
pdb|1H8E|H Chain H, (Adp.Alf4)2(Adp.So4) Bovine F1-Atpase (All Three
Catalytic Sites Occupied)
pdb|2CK3|H Chain H, Azide Inhibited Bovine F1-Atpase
pdb|2JDI|H Chain H, Ground State Structure Of F1-Atpase From Bovine Heart
Mitochondria (Bovine F1-Atpase Crystallised In The
Absence Of Azide)
pdb|2V7Q|H Chain H, The Structure Of F1-Atpase Inhibited By I1-60his, A
Monomeric Form Of The Inhibitor Protein, If1.
pdb|2WSS|H Chain H, The Structure Of The Membrane Extrinsic Region Of Bovine
Atp Synthase
pdb|2WSS|Q Chain Q, The Structure Of The Membrane Extrinsic Region Of Bovine
Atp Synthase
pdb|4ASU|H Chain H, F1-Atpase In Which All Three Catalytic Sites Contain
Bound Nucleotide, With Magnesium Ion Released In The
Empty Site
Length = 146
Score = 35.0 bits (79), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 1 MRIDIVSIEGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXX 60
M S + F++ N+ + +P + G G+ H P + ++PG
Sbjct: 16 MSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRPGL-VVVHAEDGTTSK 74
Query: 61 XFVSGGIIDIQPD-SVIVLADTAI 83
FVS G + + D SV +LA+ A+
Sbjct: 75 YFVSSGSVTVNADSSVQLLAEEAV 98
>pdb|2W6I|H Chain H, Low Resolution Structures Of Bovine Mitochondrial
F1-Atpase During Controlled Dehydration: Hydration State
4b.
pdb|2W6J|H Chain H, Low Resolution Structures Of Bovine Mitochondrial
F1-Atpase During Controlled Dehydration: Hydration State
5.
pdb|2W6H|H Chain H, Low Resolution Structures Of Bovine Mitochondrial
F1-Atpase During Controlled Dehydration: Hydration State
4a
Length = 168
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 1 MRIDIVSIEGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXX 60
M S + F++ N+ + +P + G G+ H P + ++PG
Sbjct: 38 MSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRPGL-VVVHAEDGTTSK 96
Query: 61 XFVSGGIIDIQPD-SVIVLADTAI 83
FVS G + + D SV +LA+ A+
Sbjct: 97 YFVSSGSVTVNADSSVQLLAEEAV 120
>pdb|2RQ7|A Chain A, Solution Structure Of The Epsilon Subunit Chimera
Combining The N-Terminal Beta-Sandwich Domain From T.
Elongatus Bp-1 F1 And The C-Terminal Alpha-Helical
Domain From Spinach Chloroplast F1
Length = 134
Score = 34.3 bits (77), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 19 EFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXXFVSGGIIDIQPDSVIVL 78
E ++LP G LG+ H+PL+T ++ G GG +++ + V +L
Sbjct: 20 EEVILPSTTGQLGILSNHAPLLTALETGVMRVRQDREWVAIALM--GGFAEVENNEVTIL 77
Query: 79 ADTAIHG 85
+ A G
Sbjct: 78 VNGAERG 84
>pdb|2RQ6|A Chain A, Solution Structure Of The Epsilon Subunit Of The
F1-Atpase From Thermosynechococcus Elongatus Bp-1
Length = 138
Score = 32.7 bits (73), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 19 EFIVLPGELGDLGVYPLHSPLITCIKPGFXXXXXXXXXXXXXXFVSGGIIDIQPDSVIVL 78
E ++LP G LG+ H+PL+T ++ G GG +++ + V +L
Sbjct: 20 EEVILPSTTGQLGILSNHAPLLTALETGVMRVRQDREWVAIALM--GGFAEVENNEVTIL 77
Query: 79 ADTAIHG 85
+ A G
Sbjct: 78 VNGAERG 84
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 25.8 bits (55), Expect = 8.6, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 9 EGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITC 42
EG S +++ F++ E G++ P+ SPL TC
Sbjct: 1162 EGRYLSLEDVHFLIKAAEAGEVREVPVRSPL-TC 1194
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 25.8 bits (55), Expect = 8.6, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 9 EGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITC 42
EG S +++ F++ E G++ P+ SPL TC
Sbjct: 902 EGRYLSLEDVHFLIKAAEAGEVREVPVRSPL-TC 934
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1265
Score = 25.8 bits (55), Expect = 8.6, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 9 EGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITC 42
EG S +++ F++ E G++ P+ SPL TC
Sbjct: 903 EGRYLSLEDVHFLIKAAEAGEVREVPVRSPL-TC 935
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 25.8 bits (55), Expect = 8.6, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 9 EGLLFSNKNIEFIVLPGELGDLGVYPLHSPLITC 42
EG S +++ F++ E G++ P+ SPL TC
Sbjct: 871 EGRYLSLEDVHFLIKAAEAGEVREVPVRSPL-TC 903
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
0.324 0.145 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,062,478
Number of Sequences: 62578
Number of extensions: 83925
Number of successful extensions: 115
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 92
Number of HSP's gapped (non-prelim): 17
length of query: 139
length of database: 14,973,337
effective HSP length: 89
effective length of query: 50
effective length of database: 9,403,895
effective search space: 470194750
effective search space used: 470194750
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)