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= psy12568
(114 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2E6L|A Chain A, Structure Of Mouse Wrn Exonuclease Domain
pdb|2E6M|A Chain A, Structure Of Mouse Werner Exonuclease Domain
Length = 208
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 13 SLSTLVLKCFGKTL--NKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHD 64
SL+ LV GK L +K + SNW N PL Q YAA DA+ L +YQ L +
Sbjct: 140 SLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKLGN 193
>pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An
Exoribonuclease Involved In Structured Rna Processing
Length = 375
Score = 34.7 bits (78), Expect = 0.015, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 9 GSPQS--LSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQV 58
G P S +++V + G TL+K + ++W RPL Q YAA D + LL +
Sbjct: 111 GRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPI 162
>pdb|3CYM|A Chain A, Crystal Structure Of Protein Bad_0989 From Bifidobacterium
Adolescentis
Length = 440
Score = 34.3 bits (77), Expect = 0.020, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 26/49 (53%)
Query: 22 FGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 70
G TL K+ ++W RPL +YAALD L+++ + + RQG
Sbjct: 143 LGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELETKMRAELKRQG 191
>pdb|2FBT|A Chain A, Wrn Exonuclease
pdb|2FBV|A Chain A, Wrn Exonuclease, Mn Complex
pdb|2FBX|A Chain A, Wrn Exonuclease, Mg Complex
pdb|2FBY|A Chain A, Wrn Exonuclease, Eu Complex
pdb|2FC0|A Chain A, Wrn Exonuclease, Mn Dgmp Complex
Length = 205
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 13 SLSTLVLKCFGKTL--NKQDQFSNWENRPLRPSQISYAALDAFCLLQVY---QVLHDQCA 67
SL++LV GK L +K + SNW PL Q YAA DA+ +Y ++L D
Sbjct: 145 SLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQKLYAATDAYAGFIIYRNLEILDDTVQ 204
Query: 68 R 68
R
Sbjct: 205 R 205
>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
Length = 428
Score = 33.1 bits (74), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 27 NKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 70
NKQ Q ++W RPL +SYA D LL +Y + + +G
Sbjct: 238 NKQYQLADWRIRPLPEEMLSYARDDTHYLLYIYDKMRLEMWERG 281
>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
Length = 428
Score = 29.3 bits (64), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%)
Query: 27 NKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 70
NKQ Q ++W RPL +S A D LL +Y + + +G
Sbjct: 238 NKQYQLADWRIRPLPEEMLSAARDDTHYLLYIYDKMRLEMWERG 281
>pdb|1VG2|A Chain A, Crystal Structure Of Octaprenyl Pyrophosphate Synthase
From Hyperthermophilic Thermotoga Maritima A76y Mutant
Length = 299
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 19 LKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQC 66
L +GK L + +++NR + + + ++L A L+ +Y +LHD
Sbjct: 36 LPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLYSLLHDDV 83
>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain
pdb|2HBK|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn
pdb|2HBL|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Amp
pdb|2HBM|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Ump
Length = 410
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 5/83 (6%)
Query: 9 GSPQSLSTLVLKCFGK-TLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCA 67
G P+ +L+ F +K+ Q ++W RPL + A D LL +Y DQ
Sbjct: 196 GLPRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAAARADTHFLLNIY----DQLR 251
Query: 68 RQGIELGPLLTEVLSSHAVTTKK 90
+ IE L + S V ++
Sbjct: 252 NKLIESNKLAGVLYESRNVAKRR 274
>pdb|2GSR|A Chain A, Structure Of Porcine Class Pi Glutathione S-Transferase
pdb|2GSR|B Chain B, Structure Of Porcine Class Pi Glutathione S-Transferase
Length = 207
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 43 SQISYAALDAFCLLQVYQVLHDQCARQGIELGPLLTEVLSSHAVTTKKSTIL 94
SQIS+A + LL+++QVL+ C ++ PLL+ ++ + K L
Sbjct: 144 SQISFADYNLLDLLRIHQVLNPSC----LDAFPLLSAYVARLSARPKIKAFL 191
>pdb|1VG3|A Chain A, Crystal Structure Of Octaprenyl Pyrophosphate Synthase
From Hyperthermophilic Thermotoga Maritima A76yS77F
MUTANT
Length = 299
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 19 LKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQC 66
L +GK L + +++NR + + + ++L A L+ +Y +LHD
Sbjct: 36 LPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLYFLLHDDV 83
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
0.318 0.131 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,010,731
Number of Sequences: 62578
Number of extensions: 98825
Number of successful extensions: 177
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 167
Number of HSP's gapped (non-prelim): 10
length of query: 114
length of database: 14,973,337
effective HSP length: 77
effective length of query: 37
effective length of database: 10,154,831
effective search space: 375728747
effective search space used: 375728747
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)