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= psy7778
(117 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YU3|A Chain A, Solution Structure Of The Domain Swapped Wingedhelix In
Dna- Directed Rna Polymerase Iii 39 Kda Polypeptide
Length = 95
Score = 100 bits (248), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 48/72 (66%), Positives = 62/72 (86%)
Query: 12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
LLY++KD K+K SDN+EK+VY+IIE+AGNKGIW RD+R+KSNL T++NKILK LE
Sbjct: 19 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLE 78
Query: 72 TKKIIKAVKSVA 83
+KK+IKAVKSV+
Sbjct: 79 SKKLIKAVKSVS 90
>pdb|2DK5|A Chain A, Solution Structure Of Winged-Helix Domain In Rna
Polymerase Iii 39kda Polypeptide
Length = 91
Score = 92.0 bits (227), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 44/60 (73%), Positives = 55/60 (91%)
Query: 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83
K+K SDN+EK+VY+IIE+AGNKGIW RD+R+KSNL T++NKILK LE+KK+IKAVKSVA
Sbjct: 14 KMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVA 73
>pdb|2BDT|A Chain A, Crystal Structure Of The Putative Gluconate Kinase From
Bacillus Halodurans, Northeast Structural Genomics
Target Bhr61
Length = 189
Score = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72
KD E+ + +++EE +KGI R S+L PT LN I+K L+T
Sbjct: 124 KDEQXGERCL-ELVEEFESKGIDERYFYNTSHLQPTNLNDIVKNLKT 169
>pdb|1GGZ|A Chain A, Crystal Structure Of The Calmodulin-Like Protein (Hclp)
From Human Epithelial Cells
Length = 148
Score = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 6/60 (10%)
Query: 24 KLKDSDNEEKV--VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS 81
K+KD+DNEE++ +++ ++ GN + ++R + T+L + L E ++I+A +
Sbjct: 75 KMKDTDNEEEIREAFRVFDKDGNGFVSAAELRH----VMTRLGEKLSDEEVDEMIRAADT 130
>pdb|3IZR|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 111
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 5 GFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVY-KIIEEAGNKGIWMRDIRFKSNLMPTQL 63
G+ G + Y V K K +D+ + ++ K+ GN G+ +F+SNL PT +
Sbjct: 46 GWYAGKRIAY-----VYKAKTKSNDSTIRCIWGKVTRPHGNSGV--VRAKFRSNLPPTSM 98
Query: 64 NK 65
K
Sbjct: 99 GK 100
>pdb|2FH5|A Chain A, The Structure Of The Mammalian Srp Receptor
pdb|2GO5|1 Chain 1, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
Length = 185
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 15 KVKDPVTNEKLKDSDNEEKVVYKIIEEAGNK 45
K++ P T +K +DS+ +K V +IE G K
Sbjct: 138 KIRAPTTMKKFEDSEKAKKPVRSMIETRGEK 168
>pdb|2IZ0|A Chain A, Pex Inhibitor-Home Data
pdb|2IZ0|B Chain B, Pex Inhibitor-Home Data
pdb|2IZ0|C Chain C, Pex Inhibitor-Home Data
pdb|2IZ1|A Chain A, 6pdh Complexed With Pex Inhibitor Synchrotron Data
pdb|2IZ1|B Chain B, 6pdh Complexed With Pex Inhibitor Synchrotron Data
pdb|2IZ1|C Chain C, 6pdh Complexed With Pex Inhibitor Synchrotron Data
Length = 474
Score = 25.8 bits (55), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 24 KLKDSDNEEKVVYKIIEEAGNKG 46
K KD + E +V KI+++AGNKG
Sbjct: 243 KRKDDEGEGYIVDKILDKAGNKG 265
>pdb|2IYO|A Chain A, Structural Characterization Of A Bacterial 6pdh Reveals
Aspects Of Specificity, Mechanism And Mode Of Inhibition
Length = 472
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 24 KLKDSDNEEKVVYKIIEEAGNKG 46
K KD + E +V KI+++AGNKG
Sbjct: 241 KRKDDEGEGYIVDKILDKAGNKG 263
>pdb|2IYP|A Chain A, Product Rup
pdb|2IYP|B Chain B, Product Rup
pdb|2IYP|C Chain C, Product Rup
Length = 473
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 24 KLKDSDNEEKVVYKIIEEAGNKG 46
K KD + E +V KI+++AGNKG
Sbjct: 242 KRKDDEGEGYIVDKILDKAGNKG 264
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 0.135 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,210,006
Number of Sequences: 62578
Number of extensions: 117346
Number of successful extensions: 434
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 424
Number of HSP's gapped (non-prelim): 29
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
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: 45 (21.9 bits)