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= psy3267
(105 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From
Human High Mobility Group Protein B1
Length = 173
Score = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 28/37 (75%), Positives = 34/37 (91%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 22 SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKT 58
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 30/45 (66%), Positives = 36/45 (80%)
Query: 3 NKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
NK + +YAFFVQ REEHKKKHP+ +V FAEFSKKC+ERWK+
Sbjct: 7 NKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKT 51
>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53
Transactivation Domain Interaction And Is Regulated By
The Acidic Tail
Length = 83
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 28/37 (75%), Positives = 34/37 (91%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 14 SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKT 50
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 28/37 (75%), Positives = 34/37 (91%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 8 SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKT 44
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 30/37 (81%), Positives = 33/37 (89%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AYAFFVQ CREEHKKK+PE V FAEFSKKC+ERWK+
Sbjct: 22 AYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKT 58
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 27/37 (72%), Positives = 33/37 (89%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+YAFFVQ REEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 14 SYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKT 50
>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
Length = 767
Score = 28.1 bits (61), Expect = 1.2, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 15/61 (24%)
Query: 21 EEHKKKHP---EENVVF---AEF--------SKKCAERWKSSRIVNPFVGRKFAPVFLTF 66
EE K+HP EE +V EF S + A++ + +I NPF GR+F P ++
Sbjct: 28 EELSKQHPLPSEEPLVHHDAGEFKGLQRHHTSAEEAQKLEDGKI-NPFTGREFTPKYVDI 86
Query: 67 L 67
L
Sbjct: 87 L 87
>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
Length = 773
Score = 28.1 bits (61), Expect = 1.2, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 15/61 (24%)
Query: 21 EEHKKKHP---EENVVF---AEF--------SKKCAERWKSSRIVNPFVGRKFAPVFLTF 66
EE K+HP EE +V EF S + A++ + +I NPF GR+F P ++
Sbjct: 28 EELSKQHPLPSEEPLVHHDAGEFKGLQRHHTSAEEAQKLEDGKI-NPFTGREFTPKYVDI 86
Query: 67 L 67
L
Sbjct: 87 L 87
>pdb|2RP5|A Chain A, Solution Structure Of The Oligomerization Domain In Cep-1
pdb|2RP5|B Chain B, Solution Structure Of The Oligomerization Domain In Cep-1
Length = 136
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 45 WKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRI--LEKFDECLDYFGL 101
W +++V+ + + FLT + DS+LF N + +G I EK ++ + G+
Sbjct: 52 WVPTQVVSHILPTEGLERFLTAIKAGHDSVLFNANGIYTMGDMIREFEKHNDIFERIGI 110
>pdb|1L2M|A Chain A, Minimized Average Structure Of The N-Terminal,
Dna-Binding Domain Of The Replication Initiation
Protein From A Geminivirus (Tomato Yellow Leaf Curl
Virus-Sardinia)
pdb|1L5I|A Chain A, 30-Conformer Nmr Ensemble Of The N-Terminal, Dna-Binding
Domain Of The Replication Initiation Protein From A
Geminivirus (Tomato Yellow Leaf Curl Virus-Sardinia)
Length = 118
Score = 25.4 bits (54), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 24/56 (42%)
Query: 6 NMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNPFVGRKFAP 61
N+Q F+++CRE H+ P +++ K + +V+P F P
Sbjct: 31 NLQTPTNKLFIKICRELHENGEPHLHILIQFEGKYNCTNQRFFDLVSPTRSAHFHP 86
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
0.328 0.140 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,911,760
Number of Sequences: 62578
Number of extensions: 95363
Number of successful extensions: 248
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 240
Number of HSP's gapped (non-prelim): 11
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)