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= psy12513
(159 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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 52/93 (55%), Gaps = 2/93 (2%)
Query: 48 ALDDAAVEKQIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKY 107
AL V ++ +M AFI+ EA+EK +I+ K +++Y+IE+ + R+ ++D + K
Sbjct: 7 ALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKL 66
Query: 108 RQVELRHRTDCSNIKSEGRMNVMRLNAARWSYD 140
++ L + S I ++ R+ V L+A S D
Sbjct: 67 KKAMLSQQITKSTIANKMRLKV--LSAREQSLD 97
>pdb|2KZ9|A Chain A, Structure Of E1-69 Of Yeast V-Atpase
Length = 69
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%)
Query: 48 ALDDAAVEKQIERMVAFIQTEADEKLDDIRRKIEEDYQIERERVTRDGKASVDEEYAKKY 107
AL V ++ +M AFI+ EA+EK +I+ K +++Y+IE+ + R+ ++D + K
Sbjct: 7 ALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKL 66
Query: 108 RQV 110
++
Sbjct: 67 KKA 69
>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 = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 43/87 (49%), Gaps = 17/87 (19%)
Query: 52 AAVEKQIERMVAFIQTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKY 107
A ++IER++ E +L IRRK +++ +E R+ R+ + EE AKKY
Sbjct: 161 AYTREEIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKY 211
Query: 108 RQVELRH----RTDCSNIKSEGRMNVM 130
VEL H T I + G+ +V+
Sbjct: 212 PDVELSHMLVDSTSMQLIANPGQFDVI 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 = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 43/87 (49%), Gaps = 17/87 (19%)
Query: 52 AAVEKQIERMVAFIQTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKY 107
A ++IER++ E +L IRRK +++ +E R+ R+ + EE AKKY
Sbjct: 161 AYTREEIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKY 211
Query: 108 RQVELRH----RTDCSNIKSEGRMNVM 130
VEL H T I + G+ +V+
Sbjct: 212 PDVELSHMLVDSTSMQLIANPGQFDVI 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 = 27.7 bits (60), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 43/87 (49%), Gaps = 17/87 (19%)
Query: 52 AAVEKQIERMVAFIQTEADEKLDDIRRK----IEEDYQIERERVTRDGKASVDEEYAKKY 107
A ++IER++ E +L IRRK +++ +E R+ R+ + EE AKKY
Sbjct: 161 AYTREEIERII-----EKAFQLAQIRRKKLASVDKANVLESSRMWRE----IAEETAKKY 211
Query: 108 RQVELRH----RTDCSNIKSEGRMNVM 130
VEL H T I + G+ +V+
Sbjct: 212 PDVELSHMLVDSTAMQLIANPGQFDVI 238
>pdb|4DVZ|A Chain A, Crystal Structure Of The Helicobacter Pylori Caga
Oncoprotein
Length = 569
Score = 26.9 bits (58), Expect = 5.0, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 52 AAVEKQIERMVAFIQ--TEADEKLDDIRRKIEEDYQIERERVTRDGKASVD 100
A +++I V F++ + + KLD++ K +E +Q E E +D KA +D
Sbjct: 132 ALSQEEIRNKVDFMEFLAQNNTKLDNLSEKEKEKFQNEIEDFQKDSKAYLD 182
>pdb|4G0H|A Chain A, Crystal Structure Of The N-Terminal Domain Of Helicobacter
Pylori Caga Protein
Length = 916
Score = 26.9 bits (58), Expect = 5.1, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 52 AAVEKQIERMVAFIQ--TEADEKLDDIRRKIEEDYQIERERVTRDGKASVD 100
A +++I V F++ + + KLD++ K +E +Q E E +D KA +D
Sbjct: 392 ALSQEEIRNKVDFMEFLAQNNTKLDNLSEKEKEKFQNEIEDFQKDSKAYLD 442
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
0.319 0.134 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,253,840
Number of Sequences: 62578
Number of extensions: 154642
Number of successful extensions: 483
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 477
Number of HSP's gapped (non-prelim): 19
length of query: 159
length of database: 14,973,337
effective HSP length: 91
effective length of query: 68
effective length of database: 9,278,739
effective search space: 630954252
effective search space used: 630954252
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)