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= psy12510
(236 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DL0|J Chain J, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase
pdb|4DL0|E Chain E, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase
pdb|4EFA|E Chain E, Crystal Structure Of The Heterotrimeric Egchead Peripheral
Stalk Complex Of The Yeast Vacuolar Atpase - Second
Conformation
Length = 233
Score = 70.9 bits (172), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 39/121 (32%), Positives = 70/121 (57%)
Query: 116 ALDDAAVEKQIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKY 175
AL V ++ +M AFI+ EA+EK +I+ K +++Y+IE+ + R+ ++D + K
Sbjct: 7 ALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKL 66
Query: 176 RQVELRHRTDCSNIKSEGRMNVMRVKEDSVGKIIEEAKGRLSDITEDRTKYTEILEKLIF 235
++ L + S I ++ R+ V+ +E S+ I EE K +LS I +R +Y IL+ LI
Sbjct: 67 KKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIV 126
Query: 236 Q 236
+
Sbjct: 127 E 127
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 48/83 (57%)
Query: 2 ALDDAAVEKQIERMVAFIKTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKY 61
AL V ++ +M AFI+ EA+EK +I+ K +++Y+IE+ + R+ ++D + K
Sbjct: 7 ALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKL 66
Query: 62 RQVELRHRTDCSNIKSEGRMNVM 84
++ L + S I ++ R+ V+
Sbjct: 67 KKAMLSQQITKSTIANKMRLKVL 89
>pdb|2KZ9|A Chain A, Structure Of E1-69 Of Yeast V-Atpase
Length = 69
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%)
Query: 2 ALDDAAVEKQIERMVAFIKTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKY 61
AL V ++ +M AFI+ EA+EK +I+ K +++Y+IE+ + R+ ++D + K
Sbjct: 7 ALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKL 66
Query: 62 RQV 64
++
Sbjct: 67 KKA 69
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%)
Query: 116 ALDDAAVEKQIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKY 175
AL V ++ +M AFI+ EA+EK +I+ K +++Y+IE+ + R+ ++D + K
Sbjct: 7 ALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKL 66
Query: 176 RQV 178
++
Sbjct: 67 KKA 69
>pdb|4DT0|A Chain A, The Structure Of The Peripheral Stalk Subunit E From
Pyrococcus Horikoshii
Length = 208
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 27/113 (23%), Positives = 52/113 (46%), Gaps = 11/113 (9%)
Query: 110 PTLLGMALDDAAVEKQIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDE 169
P G L + K+ ER + +I EA ++ + I+ + + + + E + R K
Sbjct: 9 PMANGAELIIQEINKEAERKIEYILNEARQQAEKIKEEARRNAEAKAEWIIRRAKT---- 64
Query: 170 EYAKKYRQVELRHRTDCSNIKSEGRMNVMRVKEDSVGKIIEEAKGRLSDITED 222
Q EL + +N + E R + ++E+ + ++EE K RL ++ED
Sbjct: 65 -------QAELEKQRIIANARLEVRRKRLAIQEEIISSVLEEVKRRLETMSED 110
>pdb|1V53|A Chain A, The Crystal Structure Of 3-Isopropylmalate Dehydrogenase
From Bacillus Coagulans
pdb|1V53|B Chain B, The Crystal Structure Of 3-Isopropylmalate Dehydrogenase
From Bacillus Coagulans
Length = 366
Score = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 18/95 (18%)
Query: 125 QIERMVAFIQTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKYRQVEL 180
+IER++ E +L IRRK +++ +E R+ R+ + EE AKKY VEL
Sbjct: 166 EIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKYPDVEL 216
Query: 181 RH----RTDCSNIKSEGRMNVMRVKEDSVGKIIEE 211
H T I + G+ +V+ V E+ G I+ +
Sbjct: 217 SHMLVDSTSMQLIANPGQFDVI-VTENMFGDILSD 250
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 17/82 (20%)
Query: 11 QIERMVAFIKTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKYRQVEL 66
+IER++ E +L IRRK +++ +E R+ R+ + EE AKKY VEL
Sbjct: 166 EIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKYPDVEL 216
Query: 67 RH----RTDCSNIKSEGRMNVM 84
H T I + G+ +V+
Sbjct: 217 SHMLVDSTSMQLIANPGQFDVI 238
>pdb|2AYQ|A Chain A, 3-Isopropylmalate Dehydrogenase From The Moderate
Facultative Thermophile, Bacillus Coagulans
pdb|2AYQ|B Chain B, 3-Isopropylmalate Dehydrogenase From The Moderate
Facultative Thermophile, Bacillus Coagulans
Length = 366
Score = 31.2 bits (69), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 18/95 (18%)
Query: 125 QIERMVAFIQTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKYRQVEL 180
+IER++ E +L IRRK +++ +E R+ R+ + EE AKKY VEL
Sbjct: 166 EIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKYPDVEL 216
Query: 181 RH----RTDCSNIKSEGRMNVMRVKEDSVGKIIEE 211
H T I + G+ +V+ V E+ G I+ +
Sbjct: 217 SHMLVDSTSMQLIANPGQFDVI-VTENMFGDILSD 250
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 17/82 (20%)
Query: 11 QIERMVAFIKTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKYRQVEL 66
+IER++ E +L IRRK +++ +E R+ R+ + EE AKKY VEL
Sbjct: 166 EIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKYPDVEL 216
Query: 67 RH----RTDCSNIKSEGRMNVM 84
H T I + G+ +V+
Sbjct: 217 SHMLVDSTSMQLIANPGQFDVI 238
>pdb|1V5B|A Chain A, The Structure Of The Mutant, S225a And E251l, Of 3-
Isopropylmalate Dehydrogenase From Bacillus Coagulans
pdb|1V5B|B Chain B, The Structure Of The Mutant, S225a And E251l, Of 3-
Isopropylmalate Dehydrogenase From Bacillus Coagulans
pdb|1V5B|C Chain C, The Structure Of The Mutant, S225a And E251l, Of 3-
Isopropylmalate Dehydrogenase From Bacillus Coagulans
pdb|1V5B|D Chain D, The Structure Of The Mutant, S225a And E251l, Of 3-
Isopropylmalate Dehydrogenase From Bacillus Coagulans
pdb|1V5B|E Chain E, The Structure Of The Mutant, S225a And E251l, Of 3-
Isopropylmalate Dehydrogenase From Bacillus Coagulans
pdb|1V5B|F Chain F, The Structure Of The Mutant, S225a And E251l, Of 3-
Isopropylmalate Dehydrogenase From Bacillus Coagulans
pdb|1V5B|G Chain G, The Structure Of The Mutant, S225a And E251l, Of 3-
Isopropylmalate Dehydrogenase From Bacillus Coagulans
pdb|1V5B|H Chain H, The Structure Of The Mutant, S225a And E251l, Of 3-
Isopropylmalate Dehydrogenase From Bacillus Coagulans
Length = 366
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 18/95 (18%)
Query: 125 QIERMVAFIQTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKYRQVEL 180
+IER++ E +L IRRK +++ +E R+ R+ + EE AKKY VEL
Sbjct: 166 EIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKYPDVEL 216
Query: 181 RH----RTDCSNIKSEGRMNVMRVKEDSVGKIIEE 211
H T I + G+ +V+ V E+ G I+ +
Sbjct: 217 SHMLVDSTAMQLIANPGQFDVI-VTENMFGDILSD 250
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 17/82 (20%)
Query: 11 QIERMVAFIKTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKYRQVEL 66
+IER++ E +L IRRK +++ +E R+ R+ + EE AKKY VEL
Sbjct: 166 EIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKYPDVEL 216
Query: 67 RH----RTDCSNIKSEGRMNVM 84
H T I + G+ +V+
Sbjct: 217 SHMLVDSTAMQLIANPGQFDVI 238
>pdb|2DM9|A Chain A, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
pdb|2DM9|B Chain B, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
Length = 198
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 26/109 (23%), Positives = 51/109 (46%), Gaps = 11/109 (10%)
Query: 114 GMALDDAAVEKQIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAK 173
G L + K+ ER + +I EA ++ + I+ + + + + E + R K
Sbjct: 3 GAELIIQEINKEAERKIEYILNEARQQAEKIKEEARRNAEAKAEWIIRRAKT-------- 54
Query: 174 KYRQVELRHRTDCSNIKSEGRMNVMRVKEDSVGKIIEEAKGRLSDITED 222
Q EL + +N + E R + ++E+ + ++EE K RL ++ED
Sbjct: 55 ---QAELEKQRIIANARLEVRRKRLAIQEEIISSVLEEVKRRLETMSED 100
>pdb|2DMA|A Chain A, Crystal Structure Of Ph1978 From Pyrococcus Horikoshii Ot3
(Form Ii)
Length = 198
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 26/109 (23%), Positives = 50/109 (45%), Gaps = 11/109 (10%)
Query: 114 GMALDDAAVEKQIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAK 173
G L + K+ ER + +I EA ++ + I+ + + + + E + R K
Sbjct: 3 GAELIIQEINKEAERKIEYILNEARQQAEKIKEEARRNAEAKAEWIIRRAKT-------- 54
Query: 174 KYRQVELRHRTDCSNIKSEGRMNVMRVKEDSVGKIIEEAKGRLSDITED 222
Q EL + +N + E R + ++E+ + ++EE K RL +ED
Sbjct: 55 ---QAELEKQRIIANARLEVRRKRLAIQEEIISSVLEEVKRRLETXSED 100
>pdb|3VEM|A Chain A, Structural Basis Of Transcriptional Gene Silencing
Mediated By Arabidopsis Mom1
pdb|3VEM|B Chain B, Structural Basis Of Transcriptional Gene Silencing
Mediated By Arabidopsis Mom1
pdb|3VEM|C Chain C, Structural Basis Of Transcriptional Gene Silencing
Mediated By Arabidopsis Mom1
pdb|3VEM|D Chain D, Structural Basis Of Transcriptional Gene Silencing
Mediated By Arabidopsis Mom1
Length = 115
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 51 ASVDEEYAKKYRQVELRHRTDCSNIKSEGRMNVMRKLC 88
A V E+ +K+ +VE H T + I+ + + +M KL
Sbjct: 71 AEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLL 108
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 0.132 0.356
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,331,851
Number of Sequences: 62578
Number of extensions: 245961
Number of successful extensions: 872
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 841
Number of HSP's gapped (non-prelim): 58
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
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: 50 (23.9 bits)