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= 026832
(232 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 71.2 bits (173), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 34/69 (49%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 104 SDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
S N PKRPP+ FFLF +FR + K +P + VAK+ GE W N+ D EK+PY+ KA
Sbjct: 5 SSGNAPKRPPSGFFLFCSEFRPKIKSTNPGIS-IGDVAKKLGEMWNNLNDSEKQPYITKA 63
Query: 164 AELKADYSK 172
A+LK Y K
Sbjct: 64 AKLKEKYEK 72
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 32/71 (45%), Positives = 43/71 (60%), Gaps = 1/71 (1%)
Query: 102 KDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLD 161
K D N PKRPP+AFFLF ++R + K HP + AK+ GE W + ++K+PY
Sbjct: 2 KKKDPNAPKRPPSAFFLFCSEYRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQ 60
Query: 162 KAAELKADYSK 172
KAA+LK Y K
Sbjct: 61 KAAKLKEKYEK 71
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 46/117 (39%), Positives = 63/117 (53%), Gaps = 1/117 (0%)
Query: 56 SCSLDAKIKMNLEAQVVEKPAEINKKKPAERKKPTSTEPRAKRLRKKDSDSNKPKRPPTA 115
S L + KM EA+ E K + R+K + + R +KK D N PKRPP+A
Sbjct: 36 SKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSA 95
Query: 116 FFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSK 172
FFLF ++R + K HP + VAK+ GE W N ++K+PY KAA+LK Y K
Sbjct: 96 FFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEK 151
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 105 DSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAA 164
D N PKRPP+AFFLF + R + K HP + AK+ GE W + ++K+PY KAA
Sbjct: 4 DPNAPKRPPSAFFLFCSEHRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQKAA 62
Query: 165 ELKADYSK 172
+LK Y K
Sbjct: 63 KLKEKYEK 70
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 57.8 bits (138), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 39/88 (44%), Positives = 53/88 (60%), Gaps = 2/88 (2%)
Query: 85 ERKKPTSTEPRAKRLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEA 144
ER+ T P+ + +KK D N PKRPP+AFFLF ++R + K HP + VAK+
Sbjct: 79 EREMKTYIPPKGE-TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKL 136
Query: 145 GEKWKNMTDEEKKPYLDKAAELKADYSK 172
GE W N ++K+PY KAA+LK Y K
Sbjct: 137 GEMWNNTAADDKQPYEKKAAKLKEKYEK 164
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 105 DSNKPKRPPTAFFLFMDDFRKEYKEAHPD-SKGVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
D KP+ +++ F+ R+E+K+ HPD S + +K+ E+WK M+ +EK + D A
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 71
Query: 164 AELKADYSKAM 174
KA Y + M
Sbjct: 72 KADKARYEREM 82
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/67 (49%), Positives = 43/67 (64%), Gaps = 1/67 (1%)
Query: 106 SNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAE 165
SN PKRPP+AFFLF ++R + K HP + VAK+ GE W N ++K+PY KAA+
Sbjct: 2 SNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 60
Query: 166 LKADYSK 172
LK Y K
Sbjct: 61 LKEKYEK 67
>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 = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/68 (48%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 105 DSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAA 164
D N PKRPP+AFFLF ++R + K HP + VAK+ GE W N ++K+PY KAA
Sbjct: 3 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 61
Query: 165 ELKADYSK 172
+LK Y K
Sbjct: 62 KLKEKYEK 69
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/64 (48%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 109 PKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKA 168
PKRPP+AFFLF ++R + K HP + VAK+ GE W N ++K+PY KAA+LK
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 61
Query: 169 DYSK 172
Y K
Sbjct: 62 KYEK 65
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 50.4 bits (119), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 46/76 (60%), Gaps = 6/76 (7%)
Query: 106 SNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAE 165
S+KPKRP +A+ L+++ R+ K +P K VT VAK GE W+ M D K + KAA+
Sbjct: 2 SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD--KSEWEAKAAK 58
Query: 166 LKADYSKAM---EGNG 178
K DY +A+ E NG
Sbjct: 59 AKDDYDRAVKEFEANG 74
>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 = 50.4 bits (119), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 46/76 (60%), Gaps = 6/76 (7%)
Query: 106 SNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAE 165
S+KPKRP +A+ L+++ R+ K +P K VT VAK GE W+ M D K + KAA+
Sbjct: 1 SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD--KSEWEAKAAK 57
Query: 166 LKADYSKAM---EGNG 178
K DY +A+ E NG
Sbjct: 58 AKDDYDRAVKEFEANG 73
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 46/76 (60%), Gaps = 6/76 (7%)
Query: 106 SNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAE 165
S+KPKRP +A+ L+++ R+ K +P K VT VAK GE W+ M D K + KAA+
Sbjct: 1 SDKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD--KSEWEAKAAK 57
Query: 166 LKADYSKAM---EGNG 178
K DY +A+ E NG
Sbjct: 58 AKDDYDRAVKEFEANG 73
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 45/75 (60%), Gaps = 6/75 (8%)
Query: 107 NKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAEL 166
+KPKRP +A+ L+++ R+ K +P K VT VAK GE W+ M D K + KAA+
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD--KSEWEAKAAKA 58
Query: 167 KADYSKAM---EGNG 178
K DY +A+ E NG
Sbjct: 59 KDDYDRAVKEFEANG 73
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 106 SNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAE 165
S+ PKR TAF L+++D R+ K +P K VT +AK+ GE WK + D+ K + D AA+
Sbjct: 1 SHMPKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELKDKSK--WEDAAAK 57
Query: 166 LKADYSKAM 174
K Y M
Sbjct: 58 DKQRYHDEM 66
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 5/62 (8%)
Query: 107 NKPKRPPTAFFLFMDDFRKEYKEAHP--DSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAA 164
NK KRP AF LF +R EY + +P D++ ++ + G++WK M +EE++ Y +A
Sbjct: 16 NKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVI---LGDRWKKMKNEERRMYTLEAK 72
Query: 165 EL 166
L
Sbjct: 73 AL 74
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 97 KRLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPD-SKGVTGVAKEAGEKWKNMTDEE 155
+R RK D N PKR +++ F + R E +P+ +K V + K G W ++DEE
Sbjct: 11 RRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEE 70
Query: 156 KKPY 159
KKPY
Sbjct: 71 KKPY 74
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 110 KRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAEL 166
KRP AF ++ D R++ +A PD + ++K G +WK MT+ EK+PY ++ A L
Sbjct: 6 KRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYEEQARL 61
>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 = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/59 (42%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 105 DSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
D N PKR +A+ F ++ R + +PD V K+ GEKWK +T EEK+PY KA
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKA 74
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/59 (42%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 105 DSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
D N PKR +A+ F ++ R + +PD V K+ GEKWK +T EEK+PY KA
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKA 74
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 105 DSNKPKRPPTAFFLFMDDFRKEYKEAHPDSK-GVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
D NKP+ +++ F+ R+E+K+ HPDS +K+ E+WK M+ +EK + D A
Sbjct: 5 DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMA 64
Query: 164 AELKADYSKAM 174
KA Y + M
Sbjct: 65 KSDKARYDREM 75
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 104 SDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
S S+ +RP AF ++ D RK + +PD ++K G+ WK +T EK+P++++A
Sbjct: 3 SGSSGIRRPMNAFMVWAKDERKRLAQQNPDLHNAE-LSKMLGKSWKALTLAEKRPFVEEA 61
Query: 164 AELKADY 170
L+ +
Sbjct: 62 ERLRVQH 68
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 103 DSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDK 162
S S+ PK P T + F+++ R++ + HPD + K G +W + EK+ YLD+
Sbjct: 2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPAEKQRYLDE 60
Query: 163 AAELKADYSKAM 174
A + K Y K +
Sbjct: 61 AEKEKQQYLKEL 72
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 104 SDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
S +++ +RP AF ++ D RK + +PD ++K G+ WK +T EK+P++++A
Sbjct: 2 SFTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAE-LSKMLGKSWKALTLAEKRPFVEEA 60
Query: 164 AELKADYSKAMEGNGDY 180
L+ + M+ + +Y
Sbjct: 61 ERLRVQH---MQDHPNY 74
>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 = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 104 SDSNKPKRPPTAFFLFMDDFRKEYKEAHPD-SKGVTGVAKEAGEKWKNMTDEEKKPYLDK 162
D KP+ +++ F+ R+E+K+ HPD S + +K+ E+WK M+ +EK + D
Sbjct: 3 GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDM 62
Query: 163 AAELKADYSKAM 174
A KA Y + M
Sbjct: 63 AKADKARYEREM 74
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 106 SNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAE 165
S++ KRP AF ++ R++ + +P + ++K G +WK +++ EK+P++D+A
Sbjct: 1 SDRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKR 59
Query: 166 LKADYSK 172
L+A + K
Sbjct: 60 LRALHMK 66
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 104 SDSNKPKRPPTAFFLFMDDFRKEYKEAHPD-SKGVTGVAKEAGEKWKNMTDEEKKPYLDK 162
D KP+ +++ F+ R+E+K+ HPD S + +K+ E+WK M+ +EK + D
Sbjct: 3 GDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDM 62
Query: 163 AAELKADYSKAM 174
A KA Y + M
Sbjct: 63 AKADKARYEREM 74
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 108 KPKRPPTAFFLFMDDFRKEYKEAHPD-SKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAEL 166
KP+ +++ F+ R+E+K+ HPD S + +K+ E+WK M+ +EK + D A
Sbjct: 1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60
Query: 167 KADYSKAM 174
KA Y + M
Sbjct: 61 KARYEREM 68
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 110 KRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKAD 169
+RP AF ++ D RK + +PD ++K G+ WK +T EK+P++++A L+
Sbjct: 4 RRPMNAFMVWAKDERKRLAQQNPDLHNAE-LSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 170 Y 170
+
Sbjct: 63 H 63
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 88
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 110 KRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKAD 169
KRP AF ++ R++ + +P + ++K G +WK +++ EK+P++D+A L+A
Sbjct: 9 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRLRAL 67
Query: 170 YSK 172
+ K
Sbjct: 68 HMK 70
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 110 KRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKAD 169
KRP AF ++ R++ + +P + ++K G +WK +++ EK+P++D+A L+A
Sbjct: 4 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRLRAL 62
Query: 170 YSK 172
+ K
Sbjct: 63 HMK 65
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 104 SDSNKPKRPPTAFFLFMDDFRKEYKEAHP--DSKGVTGVAKEAGEKWKNMTDEEKKPYLD 161
S S+ +RP AF LF R ++ HP D++G T K + W + +EK+ Y D
Sbjct: 3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGAT---KILADWWAVLDPKEKQKYTD 59
Query: 162 KAAELKADYSKAMEG 176
A E K + KA G
Sbjct: 60 MAKEYKDAFMKANPG 74
>pdb|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription Factor
Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS AT 2.77
A RESOLUTION
Length = 106
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 103 DSDSNKP--KRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYL 160
S NKP KRP AF ++ R++ + +P ++K G+ W+ + + EK+P++
Sbjct: 22 QSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAE-LSKTLGKLWRLLNESEKRPFV 80
Query: 161 DKAAELKADYSK 172
++A L+ + K
Sbjct: 81 EEAERLRVQHKK 92
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 110 KRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELK-- 167
KRP AF ++ R++ E PD ++K G++WK + D +K P++ +A L+
Sbjct: 4 KRPMNAFMVWSQIERRKIMEQSPDMHNAE-ISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62
Query: 168 --ADY 170
ADY
Sbjct: 63 HMADY 67
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 106 SNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAE 165
S KPKRP +A F+F ++ R++ +E P+ + + + W ++++++K Y + A
Sbjct: 18 SEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAA 76
Query: 166 LKAD 169
LKA
Sbjct: 77 LKAQ 80
>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Factor A, Tfam Or Mttfa, Bound To The Light Strand
Promoter Lsp
pdb|3TQ6|B Chain B, Crystal Structure Of Human Mitochondrial Transcription
Factor A, Tfam Or Mttfa, Bound To The Light Strand
Promoter Lsp
Length = 214
Score = 35.4 bits (80), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 107 NKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAEL 166
KPKRP +A+ +++ + +E K P K K E WKN++D EK+ Y+ A E
Sbjct: 113 GKPKRPRSAYNVYVAERFQEAKGDSPQEK-----LKTVKENWKNLSDSEKELYIQHAKED 167
Query: 167 KADYSKAM 174
+ Y M
Sbjct: 168 ETRYHNEM 175
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 109 PKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLD 161
PK+P +++ F + +K +PD+K T + + ++W+ + D +KK Y D
Sbjct: 10 PKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQD 61
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 108 KPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELK 167
KPKRP +A+ +++ + +E K P K K E WKN++D EK+ Y+ A E +
Sbjct: 2 KPKRPRSAYNVYVAERFQEAKGDSPQEK-----LKTVKENWKNLSDSEKELYIQHAKEDE 56
Query: 168 ADYSKAM 174
Y M
Sbjct: 57 TRYHNEM 63
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 35.0 bits (79), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 107 NKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAEL 166
KPKRP +A+ +++ + +E K P K K E WKN++D EK+ Y+ A E
Sbjct: 145 GKPKRPRSAYNVYVAERFQEAKGDSPQEK-----LKTVKENWKNLSDSEKELYIQHAKED 199
Query: 167 KADY 170
+ Y
Sbjct: 200 ETRY 203
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 109 PKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLD 161
PK+P +++ F + +K +PD+K T + + ++W+ + D +KK Y D
Sbjct: 42 PKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQD 93
>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 = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 105 DSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAA 164
D N+P++P +A+ LF D + K +P++ V+K W + +E+K+ Y K
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNPNAT-FGEVSKIVASMWDGLGEEQKQVYKKKTE 72
Query: 165 ELKADYSKAM 174
K +Y K +
Sbjct: 73 AAKKEYLKQL 82
>pdb|3V09|A Chain A, Crystal Structure Of Rabbit Serum Albumin
Length = 584
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 31/78 (39%), Gaps = 14/78 (17%)
Query: 118 LFMDDFRKEYKEAHPDSKGV----TGVAKEAGEKWKNMTD----------EEKKPYLDKA 163
LF+ F EY HPD V G A EA K TD +E +P +D+
Sbjct: 325 LFLGKFLYEYSRRHPDYSVVLLLRLGKAYEATLKKCCATDDPHACYAKVLDEFQPLVDEP 384
Query: 164 AELKADYSKAMEGNGDYN 181
L + E GDYN
Sbjct: 385 KNLVKQNCELYEQLGDYN 402
>pdb|4F5V|A Chain A, Crystal Structure Of Leporine Serum Albumin
Length = 584
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 31/78 (39%), Gaps = 14/78 (17%)
Query: 118 LFMDDFRKEYKEAHPDSKGV----TGVAKEAGEKWKNMTD----------EEKKPYLDKA 163
LF+ F EY HPD V G A EA K TD +E +P +D+
Sbjct: 325 LFLGKFLYEYSRRHPDYSVVLLLRLGKAYEATLKKCCATDDPHACYAKVLDEFQPLVDEP 384
Query: 164 AELKADYSKAMEGNGDYN 181
L + E GDYN
Sbjct: 385 KNLVKQNCELYEQLGDYN 402
>pdb|2FJI|1 Chain 1, Crystal Structure Of The C-Terminal Domain Of The Exocyst
Subunit Sec6p
pdb|2FJI|2 Chain 2, Crystal Structure Of The C-Terminal Domain Of The Exocyst
Subunit Sec6p
Length = 399
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 122 DFRKEYKEAHPDSK--GVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEGNG 178
D ++Y E + DS+ + G+ K K+++ E+K + +A E+ +Y + ME NG
Sbjct: 327 DIWQKYLEVYWDSRIDLLVGILKCR----KDVSSSERKKIVQQATEMLHEYRRNMEANG 381
>pdb|1WEO|A Chain A, Solution Structure Of Ring-Finger In The Catalytic
Subunit (Irx3) Of Cellulose Synthase
Length = 93
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 18/42 (42%)
Query: 3 SSSKSNAPKPRKRVDAQSASTSSATLMRGRDGSAFARCEECN 44
SS S+ PKP K +D Q + +G F C EC
Sbjct: 1 GSSGSSGPKPLKNLDGQFCEICGDQIGLTVEGDLFVACNECG 42
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 109 PKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYL 160
PK+P T +F F + R +Y + HP+ + + K +K+K + +++K Y+
Sbjct: 11 PKKPLTPYFRFFMEKRAKYAKLHPEMSNL-DLTKILSKKYKELPEKKKMKYI 61
>pdb|2D7L|A Chain A, Solution Structure Of The Hmg Box Domain From Human Wd
Repeat And Hmg-Box Dna Binding Protein 1
Length = 81
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%)
Query: 106 SNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
S RP T F +++++ R +PD + KE +++ ++ EE+K + +KA
Sbjct: 3 SGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKA 60
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 114 TAFFLFMDDFRKEYKEAHPDS-KGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSK 172
+A+ F+ R+E+K+ +P+ +K+ E+WK M+ +EK + + A K Y +
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 173 AMEGNG 178
M+ G
Sbjct: 81 EMKDYG 86
>pdb|3KF9|A Chain A, Crystal Structure Of The SdcenSKMLCK COMPLEX
pdb|3KF9|C Chain C, Crystal Structure Of The SdcenSKMLCK COMPLEX
Length = 149
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 41/134 (30%), Positives = 60/134 (44%), Gaps = 22/134 (16%)
Query: 56 SCSLDAK-IKMNLEAQVVEKPAEINKKKPAERKKPTST----EPRAKRLRKKDSDSNKPK 110
S ++DAK +K+ + A E E KK A+ K S E + + K + + +
Sbjct: 22 SGTIDAKELKVAMRALGFEPKKEEIKKMIADIDKDGSGTIDFEEFLQMMTAKMGERDSRE 81
Query: 111 RPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADY 170
AF LF DD + K + VAKE GE NMTDEE + +D+A
Sbjct: 82 EIMKAFRLFDDD-----ETGKISFKNLKRVAKELGE---NMTDEELQEMIDEADR----- 128
Query: 171 SKAMEGNGDYNEVE 184
+G+G+ NE E
Sbjct: 129 ----DGDGEVNEEE 138
>pdb|2F6H|X Chain X, Myosin V Cargo Binding Domain
Length = 419
Score = 26.9 bits (58), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 146 EKWKN-MTDEEKKPYLDKAAELKADY 170
E +KN MTDEE K Y+ ELK D+
Sbjct: 122 ETFKNGMTDEEYKEYVSLVTELKDDF 147
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
0.305 0.122 0.337
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,312,672
Number of Sequences: 62578
Number of extensions: 247178
Number of successful extensions: 442
Number of sequences better than 100.0: 62
Number of HSP's better than 100.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 360
Number of HSP's gapped (non-prelim): 67
length of query: 232
length of database: 14,973,337
effective HSP length: 96
effective length of query: 136
effective length of database: 8,965,849
effective search space: 1219355464
effective search space used: 1219355464
T: 11
A: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 50 (23.9 bits)