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= 047562
(246 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NA7|A Chain A, 2.2 Angstrom Structure Of The Hp0958 Protein From
Helicobacter Pylori Ccug 17874
Length = 256
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 33/102 (32%), Positives = 51/102 (50%), Gaps = 16/102 (15%)
Query: 36 NQLIFNPLEYGSDLKRPETTNIFAVNDDNSKKMKIMRRDIERHRRQEMSTLY--RSLRSL 93
N+ I N E LK + N + D N+K I ++ MS + R LRSL
Sbjct: 45 NKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKK---------MSEIKSERELRSL 95
Query: 94 LPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSEKRDELRR 135
E + +RS N+A I+NLQN I++ SEK+++L++
Sbjct: 96 NIEEDIAKERS-----NQANREIENLQNEIKRKSEKQEDLKK 132
>pdb|3E7H|A Chain A, The Crystal Structure Of The Beta Subunit Of The Dna-
Directed Rna Polymerase From Vibrio Cholerae O1 Biovar
Eltor
pdb|3E7H|B Chain B, The Crystal Structure Of The Beta Subunit Of The Dna-
Directed Rna Polymerase From Vibrio Cholerae O1 Biovar
Eltor
Length = 103
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 51 RPETTNIFAVNDDNSKKMKIMRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMN 110
R ET F + D ++ RR RH RQ + +P+EY+ GK S D++N
Sbjct: 21 RGETAT-FDIEADGKVYVEKGRRVTARHIRQLEKDGVNFIE--VPVEYIVGKVSAKDYVN 77
Query: 111 EA 112
EA
Sbjct: 78 EA 79
>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
Length = 87
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 75 IERHRRQEMSTLYRSLRSLLPLEYLKG-KRSMSDHMNEAVNYIKNLQNRIQKLSEKRDEL 133
+ER RR + + SLR +P L+G K S + +++A YI+ ++ ++ L + D+L
Sbjct: 11 LERKRRDHIKDSFHSLRDSVP--SLQGEKASRAQILDKATEYIQYMRRKVHTLQQDIDDL 68
Query: 134 RR 135
+R
Sbjct: 69 KR 70
>pdb|1OIP|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-tocopherol Transfer Protein
pdb|1OIZ|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-Tocopherol Transfer Protein
pdb|1OIZ|B Chain B, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-Tocopherol Transfer Protein
Length = 278
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 27/58 (46%)
Query: 71 MRRDIERHRRQEMSTLYRSLRSLLPLEYLKGKRSMSDHMNEAVNYIKNLQNRIQKLSE 128
++ I H +L + +LPLEY + SM D E N+I ++ + +SE
Sbjct: 218 IKERIHMHGNNYKQSLLQHFPDILPLEYGGEEFSMEDICQEWTNFIMKSEDYLSSISE 275
>pdb|2P4F|A Chain A, Crystal Structure Of Atp11 Functional Domain From Candida
Glabrata
Length = 299
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 35/83 (42%), Gaps = 11/83 (13%)
Query: 5 PSLVFPFDRTDPHD------DQLPCQQQY---HTAGQQNDNQLIFNPLEYG--SDLKRPE 53
P V P R + D D +P + QY AG + LI + EY D +P
Sbjct: 155 PLFVLPLPRENAADGNKADKDSVPVELQYVQWQFAGPNTVHCLITSLAEYKLHQDFAKPH 214
Query: 54 TTNIFAVNDDNSKKMKIMRRDIE 76
TT F ++ N K M +M +E
Sbjct: 215 TTIQFHLDLANDKDMVLMNGQVE 237
>pdb|4B6C|A Chain A, Structure Of The M. Smegmatis Gyrb Atpase Domain In
Complex With An Aminopyrazinamide
pdb|4B6C|B Chain B, Structure Of The M. Smegmatis Gyrb Atpase Domain In
Complex With An Aminopyrazinamide
Length = 196
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 158 INLEDSVTVRPCLAGVEVAINTSFRKGIPLSQVVALLAEEGLTVVNCISTKINERLLHN 216
I+ + SV VR G+ V ++ + G+P VV + + G++VVN +ST++ +L +
Sbjct: 62 IHADGSVEVRDDGRGIPVEMHAT---GMPTIDVV--MTQVGVSVVNALSTRLEATVLRD 115
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 26.9 bits (58), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 62 DDNSKKMKIMRRDIERHRRQEMSTLYRSLRSLLP 95
DD K ++ R E+ RR + + L + L S+LP
Sbjct: 6 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLP 39
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
0.317 0.133 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,156,605
Number of Sequences: 62578
Number of extensions: 212388
Number of successful extensions: 620
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 612
Number of HSP's gapped (non-prelim): 19
length of query: 246
length of database: 14,973,337
effective HSP length: 96
effective length of query: 150
effective length of database: 8,965,849
effective search space: 1344877350
effective search space used: 1344877350
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)