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= psy9636
(181 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CLY|B Chain B, Subcomplex Of The Stator Of Bovine Mitochondrial Atp
Synthase
pdb|2CLY|E Chain E, Subcomplex Of The Stator Of Bovine Mitochondrial Atp
Synthase
Length = 160
Score = 104 bits (259), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 87/154 (56%)
Query: 2 AARRFTGSKINWSELTSRLTDADRPNFNTFKAKYDGYLRKVSALPEAPPKIDWALYKNKI 61
A R+ I+W + + N+ K+ + +++ LPE PP IDWA YK +
Sbjct: 1 AGRKLALKTIDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKANV 60
Query: 62 PVPGLVDQFQKQYEALQIPFPQDTETAKINEEEKQTMAEIKKWIEESQVRIAGYKKEIED 121
GLVD F+K++ AL++P P+D TA+++ EEK+ + +++ +S+ RI Y+KE+E
Sbjct: 61 AKAGLVDDFEKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKELEK 120
Query: 122 EEALPPVSEMTMQEYCLAYPECAYDPEKPTFWPH 155
+ P +MT+++ +PE D +K +WPH
Sbjct: 121 MRNIIPFDQMTIEDLNEVFPETKLDKKKYPYWPH 154
>pdb|2WSS|U Chain U, The Structure Of The Membrane Extrinsic Region Of Bovine
Atp Synthase
Length = 118
Score = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 39/118 (33%), Positives = 68/118 (57%)
Query: 2 AARRFTGSKINWSELTSRLTDADRPNFNTFKAKYDGYLRKVSALPEAPPKIDWALYKNKI 61
A R+ I+W + + N+ K+ + +++ LPE PP IDWA YK +
Sbjct: 1 AGRKLALKTIDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKANV 60
Query: 62 PVPGLVDQFQKQYEALQIPFPQDTETAKINEEEKQTMAEIKKWIEESQVRIAGYKKEI 119
GLVD F+K++ AL++P P+D TA+++ EEK+ + +++ +S+ RI Y+KE+
Sbjct: 61 AKAGLVDDFEKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKEL 118
>pdb|4B2Q|U Chain U, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
Subtomogram Average
pdb|4B2Q|UU Chain u, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
Subtomogram Average
Length = 120
Score = 80.1 bits (196), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 38/110 (34%), Positives = 66/110 (60%)
Query: 11 INWSELTSRLTDADRPNFNTFKAKYDGYLRKVSALPEAPPKIDWALYKNKIPVPGLVDQF 70
I+W + + N+ K+ + +++ LPE PP IDWA YK + GLVD F
Sbjct: 7 IDWVAFGEIIPRNQKAVANSLKSWNETLTSRLATLPEKPPAIDWAYYKANVAKAGLVDDF 66
Query: 71 QKQYEALQIPFPQDTETAKINEEEKQTMAEIKKWIEESQVRIAGYKKEIE 120
+K++ AL++P P+D TA+++ EEK+ + +++ +S+ RI Y+KE+E
Sbjct: 67 EKKFNALKVPIPEDKYTAQVDAEEKEDVKSCAEFLTQSKTRIQEYEKELE 116
>pdb|3GR0|A Chain A, Periplasmic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-362)
pdb|3GR0|B Chain B, Periplasmic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-362)
pdb|3GR0|C Chain C, Periplasmic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-362)
pdb|3GR0|D Chain D, Periplasmic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-362)
Length = 197
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 140 YPECAY------DPEKPTFWPHDEENQITKEDEEWWEKRQKNLV 177
YP+ AY +P KP FW + N ++K++ E ++ + L+
Sbjct: 75 YPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALM 118
>pdb|2Y9J|A Chain A, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|B Chain B, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|C Chain C, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|D Chain D, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|E Chain E, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|F Chain F, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|G Chain G, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|H Chain H, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|I Chain I, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|J Chain J, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|K Chain K, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|L Chain L, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|M Chain M, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|N Chain N, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|O Chain O, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|P Chain P, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|Q Chain Q, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|R Chain R, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|S Chain S, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|T Chain T, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|U Chain U, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|V Chain V, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|W Chain W, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
pdb|2Y9J|X Chain X, Three-Dimensional Model Of Salmonella's Needle Complex At
Subnanometer Resolution
Length = 186
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 140 YPECAY------DPEKPTFWPHDEENQITKEDEEWWEKRQKNLV 177
YP+ AY +P KP FW + N ++K++ E ++ + L+
Sbjct: 64 YPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALM 107
>pdb|2GQ3|A Chain A, Mycobacterium Tuberculosis Malate Synthase In Complex With
Magnesium, Malate, And Coenzyme A
pdb|2GQ3|B Chain B, Mycobacterium Tuberculosis Malate Synthase In Complex With
Magnesium, Malate, And Coenzyme A
Length = 729
Score = 28.5 bits (62), Expect = 2.0, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 81 FPQDTETAKINEEEKQTMAEIKKWIEESQVRI----AGYKKEIEDE-----EALPPVSEM 131
PQ+T I +EE++T +K I+ + R+ G+ DE EA P V +
Sbjct: 424 LPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDEIHTSMEAGPMVRKG 483
Query: 132 TM--QEYCLAYPECAYD 146
TM Q + LAY + D
Sbjct: 484 TMKSQPWILAYEDHNVD 500
>pdb|2LD3|A Chain A, Solution Structure Of Myosin Vi Lever Arm Extension
Length = 88
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 28 FNTFKAKYDGYLRKVSALPEAPPKIDWALYKNKIPVPGLV----------DQFQKQYEAL 77
T K + D + VSAL + P+++ + +I + L+ +Q QK+Y+AL
Sbjct: 9 VGTLKKRLDKFNEVVSALKDGKPEVNRQIKNLEISIDALMAKIKSTMMTREQIQKEYDAL 68
>pdb|1N8I|A Chain A, Biochemical And Structural Studies Of Malate Synthase From
Mycobacterium Tuberculosis
pdb|1N8W|A Chain A, Biochemical And Structural Studies Of Malate Synthase From
Mycobacterium Tuberculosis
pdb|1N8W|B Chain B, Biochemical And Structural Studies Of Malate Synthase From
Mycobacterium Tuberculosis
Length = 741
Score = 28.5 bits (62), Expect = 2.3, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 81 FPQDTETAKINEEEKQTMAEIKKWIEESQVRI----AGYKKEIEDE-----EALPPVSEM 131
PQ+T I +EE++T +K I+ + R+ G+ DE EA P V +
Sbjct: 422 LPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDEIHTSMEAGPMVRKG 481
Query: 132 TM--QEYCLAYPECAYD 146
TM Q + LAY + D
Sbjct: 482 TMKSQPWILAYEDHNVD 498
>pdb|3S9I|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Malate
Synthase In Complex With 2-4-dioxo-4-phenylbutanoic Acid
Inhibitor
pdb|3S9Z|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Malate
Synthase In Complex With
4-(2-bromophenyl)-2,4-dioxobutanoic Acid Inhibitor
pdb|3SAD|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Malate
Synthase In Complex With
4-(2-mehtylphenyl)-2,4-dioxobutanoic Acid Inhibitor
pdb|3SAZ|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Malate
Synthase In Complex With
4-(3-bromophenyl)-2,4-dioxobutanoic Acid Inhibitor
pdb|3SB0|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Malate
Synthase In Complex With
4-(2-chloro-6-fluoro-3-methylphenyl)-2,4-dioxobutanoic
Acid Inhibitor
Length = 741
Score = 28.5 bits (62), Expect = 2.4, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 81 FPQDTETAKINEEEKQTMAEIKKWIEESQVRI----AGYKKEIEDE-----EALPPVSEM 131
PQ+T I +EE++T +K I+ + R+ G+ DE EA P V +
Sbjct: 422 LPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDEIHTSMEAGPMVRKG 481
Query: 132 TM--QEYCLAYPECAYD 146
TM Q + LAY + D
Sbjct: 482 TMKSQPWILAYEDHNVD 498
>pdb|1UHF|A Chain A, Solution Structure Of The Third Sh3 Domain Of Human
Intersectin 2(Kiaa1256)
Length = 69
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 134 QEYCLAYPECAYDPEKPTFWPHDEENQITKEDEEWWEKRQKNLVG 178
+EY YP + +P TF EE +T++D EWW + G
Sbjct: 9 EEYIALYPYSSVEPGDLTF-TEGEEILVTQKDGEWWTGSIGDRSG 52
>pdb|3GR1|A Chain A, Periplamic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-392)
pdb|3GR1|B Chain B, Periplamic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-392)
pdb|3GR1|C Chain C, Periplamic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-392)
pdb|3GR1|D Chain D, Periplamic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-392)
pdb|3GR1|E Chain E, Periplamic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-392)
pdb|3GR1|F Chain F, Periplamic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-392)
pdb|3GR1|G Chain G, Periplamic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-392)
pdb|3GR1|H Chain H, Periplamic Domain Of The T3ss Inner Membrane Protein Prgh
From S.Typhimurium (Fragment 170-392)
Length = 227
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 140 YPECAY------DPEKPTFWPHDEENQITKEDEEWWEKRQKNLV 177
YP+ AY +P KP FW + N ++K++ E ++ + L+
Sbjct: 75 YPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALM 118
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
Length = 66
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 77 LQIPFPQDTETAKINEEEKQTMAEIKKWIEESQVR 111
LQ FP D E ++ E +EIKKW + + R
Sbjct: 24 LQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYR 58
>pdb|3NQP|A Chain A, Crystal Structure Of A Susd Superfamily Protein (Bf1802)
From Bacteroides Fragilis Nctc 9343 At 1.90 A Resolution
pdb|3NQP|B Chain B, Crystal Structure Of A Susd Superfamily Protein (Bf1802)
From Bacteroides Fragilis Nctc 9343 At 1.90 A Resolution
Length = 514
Score = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 21/45 (46%)
Query: 135 EYCLAYPECAYDPEKPTFWPHDEENQITKEDEEWWEKRQKNLVGG 179
E AYPE A H+++ + +E + WW+ R+ L G
Sbjct: 420 ETLYAYPETADFTTNELAILHEKDKEFIQEGQRWWDLRRXTLTKG 464
>pdb|1UDL|A Chain A, The Solution Structure Of The Fifth Sh3 Domain Of
Intersectin 2 (Kiaa1256)
Length = 98
Score = 26.6 bits (57), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 102 KKWIEESQVRIAGYKKEIEDEEALPPVSEMTMQEYCLAYPECAYDPEKPTFWPHDEENQI 161
K W S V++ G E P + M +Y A + ++ +F N +
Sbjct: 9 KGWFPASHVKLLGPSSERATPAFHPVCQVIAMYDYA------ANNEDELSFSKGQLINVM 62
Query: 162 TKEDEEWWEKRQKNLVG 178
K+D +WW+ + G
Sbjct: 63 NKDDPDWWQGEINGVTG 79
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 26.6 bits (57), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 78 QIPFPQDTETAKINEEEKQTMAEIKKWIEESQVRI 112
Q P P D E ++ E K T EI W E + ++
Sbjct: 28 QNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
>pdb|2XFX|A Chain A, Cattle Mhc Class I N01301 Presenting An 11mer From
Theileria Parva
Length = 277
Score = 26.6 bits (57), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 148 EKPTFWPHDEENQITKEDEEWWEKRQKNLVG 178
E P +W D E QI+KE+ W+ + NL G
Sbjct: 55 EGPEYW--DRETQISKENALWYREALNNLRG 83
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics Consortium
(Nesg) Target Hr7907f
Length = 74
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 77 LQIPFPQDTETAKINEEEKQTMAEIKKWIEESQ 109
L+ FP D+E ++ + T EIKKW +++
Sbjct: 26 LKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTR 58
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
0.312 0.131 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,138,896
Number of Sequences: 62578
Number of extensions: 254171
Number of successful extensions: 561
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 552
Number of HSP's gapped (non-prelim): 40
length of query: 181
length of database: 14,973,337
effective HSP length: 93
effective length of query: 88
effective length of database: 9,153,583
effective search space: 805515304
effective search space used: 805515304
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)