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= 034563
(91 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 21/32 (65%), Positives = 24/32 (75%)
Query: 50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
KKDPN PKRPPSAFF+F E+R K EHP +
Sbjct: 3 KKDPNAPKRPPSAFFLFCSEYRPKIKSEHPGL 34
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/32 (65%), Positives = 23/32 (71%)
Query: 50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
KKDPN PKRPPSAFF+F E R K EHP +
Sbjct: 2 KKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGL 33
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 20/31 (64%), Positives = 23/31 (74%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
KDPN PKRPPSAFF+F E+R K EHP +
Sbjct: 97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL 127
Score = 25.4 bits (54), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
DP KP+ S++ F++ R+ +K++HP+
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDA 41
>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
pdb|1HMF|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
Length = 77
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 20/31 (64%), Positives = 23/31 (74%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
KDPN PKRPPSAFF+F E+R K EHP +
Sbjct: 2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL 32
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 20/31 (64%), Positives = 23/31 (74%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
KDPN PKRPPSAFF+F E+R K EHP +
Sbjct: 84 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL 114
>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With
Dna
pdb|1NHN|A Chain A, The Structure Of The Hmg Box And Its Interaction With
Dna
Length = 81
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 17/28 (60%), Positives = 20/28 (71%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
N PKRPPSAFF+F E+R K EHP +
Sbjct: 3 NAPKRPPSAFFLFCSEYRPKIKGEHPGL 30
>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With
Dna
pdb|1HSN|A Chain A, The Structure Of The Hmg Box And Its Interaction With
Dna
Length = 79
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/26 (61%), Positives = 19/26 (73%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNV 81
PKRPPSAFF+F E+R K EHP +
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGL 28
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From
High Mobility Group Protein B3
Length = 81
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 20/34 (58%)
Query: 48 SAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
S+ N PKRPPS FF+F EFR K +P +
Sbjct: 2 SSGSSGNAPKRPPSGFFLFCSEFRPKIKSTNPGI 35
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
+ K KPKRP SA F+F EE R+ ++E P +
Sbjct: 12 EGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPEL 46
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVK 82
+KPKRP SA+ ++L R+ K+E+P +K
Sbjct: 3 DKPKRPLSAYMLWLNSARESIKRENPGIK 31
>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna
pdb|1QRV|B Chain B, Crystal Structure Of The Complex Of Hmg-D And Dna
Length = 73
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVK 82
+KPKRP SA+ ++L R+ K+E+P +K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK 30
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVK 82
+KPKRP SA+ ++L R+ K+E+P +K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK 30
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 33.1 bits (74), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%), Gaps = 2/37 (5%)
Query: 53 PNKPKRPPSAFFVFLEEFRKVYKQEHP--NVKAVSAV 87
PNK KRP +AF +F +++R Y Q +P + +A+S +
Sbjct: 15 PNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVI 51
>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex
pdb|3NM9|D Chain D, Hmgd(M13a)-Dna Complex
pdb|3NM9|G Chain G, Hmgd(M13a)-Dna Complex
pdb|3NM9|J Chain J, Hmgd(M13a)-Dna Complex
pdb|3NM9|M Chain M, Hmgd(M13a)-Dna Complex
pdb|3NM9|P Chain P, Hmgd(M13a)-Dna Complex
Length = 73
Score = 32.0 bits (71), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVK 82
+KPKRP SA+ ++L R+ K+E+P +K
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIK 30
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb
Protein Nhp6a In Complex With Sry Dna
pdb|1LWM|A Chain A, Solution Structure Of The Sequence-Non-Specific Hmgb
Protein Nhp6a
Length = 93
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
DPN PKR SA+ F E R + + E+P++
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDI 46
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
DPN PKR SA+ F E R + + E+P++
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDI 46
>pdb|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like
Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A)
Length = 97
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV-KAVSAVS 88
AKKDPN PKR S++ F +E R E+P + K V+A+
Sbjct: 16 AKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIG 56
>pdb|2V2Q|A Chain A, Ispe In Complex With Ligand
pdb|2V2Q|B Chain B, Ispe In Complex With Ligand
pdb|2V2V|A Chain A, Ispe In Complex With Ligand
pdb|2V2V|B Chain B, Ispe In Complex With Ligand
pdb|2V2Z|A Chain A, Ispe In Complex With Adp And Cdpme
pdb|2V2Z|B Chain B, Ispe In Complex With Adp And Cdpme
pdb|2V34|A Chain A, Ispe In Complex With Cytidine And Ligand
pdb|2V34|B Chain B, Ispe In Complex With Cytidine And Ligand
pdb|2V8P|A Chain A, Ispe In Complex With Adp And Cdp
pdb|2V8P|B Chain B, Ispe In Complex With Adp And Cdp
pdb|2VF3|A Chain A, Aquifex Aeolicus Ispe In Complex With Ligand
pdb|2VF3|B Chain B, Aquifex Aeolicus Ispe In Complex With Ligand
Length = 271
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 6 GKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRT 43
GK A+ + K EV++PVE +GK V+ SS R
Sbjct: 140 GKSAIGRGKGEVLEPVETEISGKITLVIPQVSSSTGRV 177
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVSI 89
+RP +AF +F + R + +QEHP + A I
Sbjct: 9 RRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKI 41
>pdb|2CO9|A Chain A, Solution Structure Of The Hmg_box Domain Of Thymus High
Mobility Group Box Protein Tox From Mouse
Length = 102
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPN 80
DPN+P++P SA+ +F + + K ++PN
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNPN 42
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human
Upstream Binding Factor
Length = 99
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 46 VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVSI 89
+K KK P+ PK+P + +F F E R Y + HP + + I
Sbjct: 1 MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKI 44
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAV 84
PKR +AF ++L + R+ K+E+P +K
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIKVT 32
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPN 80
K DPNKP+ S++ F++ R+ +K++HP+
Sbjct: 2 GKGDPNKPRGKMSSYAFFVQTSREEHKKKHPD 33
>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 = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
K DP KP+ S++ F++ R+ +K++HP+
Sbjct: 1 GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDA 33
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV 81
K DP KP+ S++ F++ R+ +K++HP+
Sbjct: 1 GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDA 33
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
0.310 0.126 0.343
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,290,057
Number of Sequences: 62578
Number of extensions: 69935
Number of successful extensions: 224
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 185
Number of HSP's gapped (non-prelim): 39
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 45 (21.9 bits)