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= 010122
(517 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HME|A Chain A, Crystal Structure Of Human Bromodomain Containing 9
Isoform 1 (Brd9)
pdb|3HME|B Chain B, Crystal Structure Of Human Bromodomain Containing 9
Isoform 1 (Brd9)
Length = 123
Score = 37.4 bits (85), Expect = 0.023, Method: Composition-based stats.
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 8 QKDVFLICSNAMQYNAPDTIYFRQARSI 35
+ D L+C NAM YN PDT+Y++ A+ I
Sbjct: 75 KADFKLMCDNAMTYNRPDTVYYKLAKKI 102
>pdb|2D9E|A Chain A, Solution Structure Of The Bromodomain Of Peregrin
pdb|2RS9|B Chain B, Solution Structure Of The Bromodomain Of Human Brpf1 In
Complex With Histone H4k5ac Peptide
Length = 121
Score = 35.0 bits (79), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 8 QKDVFLICSNAMQYNAPDTIYFRQARSIHE 37
++D LI SN ++YNA DTI++R A + E
Sbjct: 69 EEDFNLIVSNCLKYNAKDTIFYRAAVRLRE 98
>pdb|2I7K|A Chain A, Solution Structure Of The Bromodomain Of Human Brd7
Protein
Length = 117
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 15/28 (53%), Positives = 22/28 (78%), Gaps = 1/28 (3%)
Query: 9 KDVF-LICSNAMQYNAPDTIYFRQARSI 35
KD F L+C+NAM YN P+TIY++ A+ +
Sbjct: 70 KDNFKLMCTNAMIYNKPETIYYKAAKKL 97
>pdb|3RCW|A Chain A, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|B Chain B, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|C Chain C, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|D Chain D, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|E Chain E, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|F Chain F, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|G Chain G, Crystal Structure Of The Bromodomain Of Human Brd1
pdb|3RCW|H Chain H, Crystal Structure Of The Bromodomain Of Human Brd1
Length = 135
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 8 QKDVFLICSNAMQYNAPDTIYFRQARSIHELAKKNFENLRQDSD 51
++D LI N M+YNA DT+++R A + + R++ D
Sbjct: 75 EEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVD 118
>pdb|4DNV|A Chain A, Crystal Structure Of The W285f Mutant Of Uvb-Resistance
Protein Uvr8
pdb|4DNV|B Chain B, Crystal Structure Of The W285f Mutant Of Uvb-Resistance
Protein Uvr8
pdb|4DNV|C Chain C, Crystal Structure Of The W285f Mutant Of Uvb-Resistance
Protein Uvr8
pdb|4DNV|D Chain D, Crystal Structure Of The W285f Mutant Of Uvb-Resistance
Protein Uvr8
Length = 370
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 278 LSSASTHSTIELKGDKLTERPEAED-------SSEKPGPSTQSSLDGH 318
+S+ ++HS L GD + ED + ++P P+ S+LDGH
Sbjct: 9 ISAGASHSVALLSGDIVCSWGRGEDGQLGHGDAEDRPSPTQLSALDGH 56
>pdb|4DNW|A Chain A, Crystal Structure Of Uvb-Resistance Protein Uvr8
pdb|4DNW|B Chain B, Crystal Structure Of Uvb-Resistance Protein Uvr8
Length = 374
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 278 LSSASTHSTIELKGDKLTERPEAED-------SSEKPGPSTQSSLDGH 318
+S+ ++HS L GD + ED + ++P P+ S+LDGH
Sbjct: 9 ISAGASHSVALLSGDIVCSWGRGEDGQLGHGDAEDRPSPTQLSALDGH 56
>pdb|4DNU|A Chain A, Crystal Structure Of The W285a Mutant Of Uvb-Resistance
Protein Uvr8
Length = 372
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 278 LSSASTHSTIELKGDKLTERPEAED-------SSEKPGPSTQSSLDGH 318
+S+ ++HS L GD + ED + ++P P+ S+LDGH
Sbjct: 11 ISAGASHSVALLSGDIVCSWGRGEDGQLGHGDAEDRPSPTQLSALDGH 58
>pdb|4D9S|A Chain A, Crystal Structure Of Arabidopsis Thaliana Uvr8 (Uv
Resistance Locus 8)
pdb|4D9S|B Chain B, Crystal Structure Of Arabidopsis Thaliana Uvr8 (Uv
Resistance Locus 8)
Length = 406
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 278 LSSASTHSTIELKGDKLTERPEAED-------SSEKPGPSTQSSLDGH 318
+S+ ++HS L GD + ED + ++P P+ S+LDGH
Sbjct: 21 ISAGASHSVALLSGDIVCSWGRGEDGQLGHGDAEDRPSPTQLSALDGH 68
>pdb|1OKJ|A Chain A, Crystal Structure Of The Essential E. Coli Yeaz Protein By
Mad Method Using The Gadolinium Complex "dotma"
pdb|1OKJ|B Chain B, Crystal Structure Of The Essential E. Coli Yeaz Protein By
Mad Method Using The Gadolinium Complex "dotma"
pdb|1OKJ|C Chain C, Crystal Structure Of The Essential E. Coli Yeaz Protein By
Mad Method Using The Gadolinium Complex "dotma"
pdb|1OKJ|D Chain D, Crystal Structure Of The Essential E. Coli Yeaz Protein By
Mad Method Using The Gadolinium Complex "dotma"
Length = 251
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 38/97 (39%), Gaps = 24/97 (24%)
Query: 196 LMTV--GLHSEHGYTRSLARFAANLGPVAW----------------------KIAARRIE 231
LMT+ G ++G TR LA A +G V W +I R++
Sbjct: 115 LMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQ 174
Query: 232 RCLPAGVRFGPGWVVENDLAPQRPLLLSSATVGLPSS 268
+ V G GW DL + L+L V LP++
Sbjct: 175 QLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAA 211
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
0.312 0.130 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,054,365
Number of Sequences: 62578
Number of extensions: 677683
Number of successful extensions: 1215
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1208
Number of HSP's gapped (non-prelim): 17
length of query: 517
length of database: 14,973,337
effective HSP length: 103
effective length of query: 414
effective length of database: 8,527,803
effective search space: 3530510442
effective search space used: 3530510442
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)