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= psy12253
(149 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NGQ|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain
Length = 398
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 38/77 (49%), Gaps = 12/77 (15%)
Query: 69 LTSAYRHRTANNQEPQYTTWKIREEGEVCHTIDYVFYSQDKFDVEAVLDMPSGEQIGRDR 128
L SAY NN P YT + +G IDY+FYS+ +VE VL + + +
Sbjct: 309 LKSAYE----NNLMP-YTNYTFDFKG----VIDYIFYSKTHMNVEGVLGPLDPQWLVENN 359
Query: 129 I---PSLRYPSDHFSLV 142
I P PSDHFSL+
Sbjct: 360 ITGCPHPHIPSDHFSLL 376
>pdb|3NGN|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
Complex With Amp
pdb|3NGO|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
Complex With Poly(A) Dna
Length = 398
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 37/77 (48%), Gaps = 12/77 (15%)
Query: 69 LTSAYRHRTANNQEPQYTTWKIREEGEVCHTIDYVFYSQDKFDVEAVLDMPSGEQIGRDR 128
L SAY NN P YT + +G IDY+FYS+ +V VL + + +
Sbjct: 309 LKSAYE----NNLMP-YTNYTFDFKG----VIDYIFYSKTHMNVLGVLGPLDPQWLVENN 359
Query: 129 I---PSLRYPSDHFSLV 142
I P PSDHFSL+
Sbjct: 360 ITGCPHPHIPSDHFSLL 376
>pdb|4GZ2|A Chain A, Mus Musculus Tdp2 Excluded Ssdna Complex
pdb|4GZ2|B Chain B, Mus Musculus Tdp2 Excluded Ssdna Complex
Length = 255
Score = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 98 HTIDYVFYSQDKFDVEAVLDMPSGEQIGRDRIPSLRYPSDHFSLVCDLTL 147
H D +F+ + E L S + +G +++ R+PSDH+ L+C L +
Sbjct: 209 HRFDRIFFRAE----EGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNV 254
>pdb|4GYZ|A Chain A, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|B Chain B, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|C Chain C, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|D Chain D, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|E Chain E, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|F Chain F, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|G Chain G, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|H Chain H, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|I Chain I, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GZ0|A Chain A, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|B Chain B, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|E Chain E, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|K Chain K, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|G Chain G, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|I Chain I, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ1|A Chain A, Mus Musculus Tdp2 Reaction Product (5'-Phosphorylated
Dna)-Mg2+ Complex At 1.5 Angstroms Resolution
pdb|4GZ1|B Chain B, Mus Musculus Tdp2 Reaction Product (5'-Phosphorylated
Dna)-Mg2+ Complex At 1.5 Angstroms Resolution
Length = 256
Score = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 98 HTIDYVFYSQDKFDVEAVLDMPSGEQIGRDRIPSLRYPSDHFSLVCDLTL 147
H D +F+ + E L S + +G +++ R+PSDH+ L+C L +
Sbjct: 209 HRFDRIFFRAE----EGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNV 254
>pdb|4GSK|Y Chain Y, Crystal Structure Of An Atg7-Atg10 Crosslinked Complex
pdb|4GSK|Z Chain Z, Crystal Structure Of An Atg7-Atg10 Crosslinked Complex
Length = 173
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 56/117 (47%), Gaps = 21/117 (17%)
Query: 39 RNGALLSTL--RNEQEPTEPIYNTVMNHETLGLTSAYRHRTANNQEPQYTTWKIREEGEV 96
++G LL + R Q+ TE I N ++NH L LT + + EP +I EE
Sbjct: 41 KDGLLLRLIPTRQLQKNTERIENKLLNHIELYLTYSKVYN-----EPLLLL-RIWEE--- 91
Query: 97 CHTIDYVFYSQDKF--DVEAVLDMPSGEQIGRDRIPSLR-------YPSDHFSLVCD 144
+ID + ++ D+E++LD+ Q+G D I +L +P D S+V D
Sbjct: 92 -KSIDGIPMTKLMLPTDIESLLDVQGKFQLGLDTIINLEGSVWYSFHPCDTSSIVGD 147
>pdb|1F1S|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase At 2.1 Angstrom Resolution.
pdb|1I8Q|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Enzyme Product, Unsaturated
Disaccharide Hyaluronan
pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Hexasaccharide Unit Of Hyaluronan
Length = 814
Score = 26.9 bits (58), Expect = 4.3, Method: Composition-based stats.
Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 27 EEICIATTHLKARNGA--LLSTLRNEQEPTEPIYNTVMNHETLGLTSAYRHRTANNQEPQ 84
++I +++K NG + +T+ ++ ++ Y T +N +T+ L + A++Q+
Sbjct: 600 DKIVFLGSNIKNTNGIGNVSTTIDQRKDDSKTPYTTYVNGKTIDL------KQASSQQFT 653
Query: 85 YTTWKIREEGEVCHTIDYVFYSQDKFDVE 113
T E E I Y+F+ D+E
Sbjct: 654 DTKSVFLESKEPGRNIGYIFFKNSTIDIE 682
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 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,322,139
Number of Sequences: 62578
Number of extensions: 169385
Number of successful extensions: 639
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 634
Number of HSP's gapped (non-prelim): 7
length of query: 149
length of database: 14,973,337
effective HSP length: 90
effective length of query: 59
effective length of database: 9,341,317
effective search space: 551137703
effective search space used: 551137703
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)