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= 020402
(326 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KK0|A Chain A, Solution Structure Of Dead Ringer-Like Protein 1 (At-Rich
Interactive Domain-Containing Protein 3a) From Homo
Sapiens, Northeast Structural Genomics Consortium (Nesg)
Target Hr4394c
Length = 145
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 29/66 (43%), Positives = 43/66 (65%)
Query: 68 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 127
++P + + LDL L+V VT +GGL +VI + W+E+ N PT+ITSA+F LR Y+
Sbjct: 55 RIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMK 114
Query: 128 LLYHFE 133
LY +E
Sbjct: 115 YLYPYE 120
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead
Ringer Protein
Length = 128
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 42/66 (63%)
Query: 68 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 127
++P + LDL+ L+ V +RGGL VI + W+E++ + P++ITSA+F LR Y+
Sbjct: 43 RLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAAFTLRTQYMK 102
Query: 128 LLYHFE 133
LY +E
Sbjct: 103 YLYPYE 108
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex
Length = 139
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 41/66 (62%)
Query: 68 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 127
++P + LDL+ L+ V +RGGL VI + W+E++ + P++ITSA+ LR Y+
Sbjct: 45 RLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAALTLRTQYMK 104
Query: 128 LLYHFE 133
LY +E
Sbjct: 105 YLYPYE 110
>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid
Length = 120
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 42/65 (64%), Gaps = 1/65 (1%)
Query: 69 VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSL 128
+P VG K LDL+RL+V V GGL +V ++++W+E+ N T +SA+ L+K Y+
Sbjct: 42 LPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNV-GTSSSAASSLKKQYIQC 100
Query: 129 LYHFE 133
LY FE
Sbjct: 101 LYAFE 105
>pdb|2CXY|A Chain A, Crystal Structure Of The Hbaf250b At-Rich Interaction
Domain (Arid)
pdb|2EH9|A Chain A, Crystal Structure Of The Hbaf250b At-Rich Interaction
Domain (Arid)
Length = 125
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 69 VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSL 128
+P VG K LDL RL+V V GGL +V ++++W+E+ N T +SA+ L+K Y+
Sbjct: 43 LPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNV-GTSSSAASSLKKQYIQY 101
Query: 129 LYHFE 133
L+ FE
Sbjct: 102 LFAFE 106
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKA-ISKKIGVLWSNLTEAEKQVYQEKGLK 304
DP+ PK S + F +EH ++K + G +KK+G +WS + +KQ Y++K K
Sbjct: 4 DPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAK 63
Query: 305 DKERYKSEMLEYRS 318
KE+Y+ ++ YR+
Sbjct: 64 LKEKYEKDIAAYRA 77
>pdb|2LM1|A Chain A, Solution Nmr Structure Of Lysine-Specific Demethylase Lid
From Drosophila Melanogaster, Northeast Structural
Genomics Consortium Target Fr824d
Length = 107
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 52 FWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFP 111
F + F + G K+P V KALDL+ L V GG+ + +DR+W +V +P
Sbjct: 19 FLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKDRKWAKVANRMQYP 78
Query: 112 TTITSASFVLRKYYLSLLYHFE 133
++ S L+ +Y +L+ FE
Sbjct: 79 SS-KSVGATLKAHYERILHPFE 99
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 250 PKSNRSGYNFFFAEHYARLKPHYYGQEKA-ISKKIGVLWSNLTEAEKQVYQEKGLKDKER 308
PK SG+ F +E ++K G ++KK+G +W+NL ++EKQ Y K K KE+
Sbjct: 10 PKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEK 69
Query: 309 YKSEMLEYRS 318
Y+ ++ +Y+S
Sbjct: 70 YEKDVADYKS 79
>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN
Jarid1c Protein
Length = 117
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 59 FHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSAS 118
F + G K+P V + LDL+ L V GG + +DRRW V N+P S
Sbjct: 22 FWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKDRRWARVAQRLNYPPGKNIGS 81
Query: 119 FVLRKYYLSLLYHFE 133
LR +Y ++Y +E
Sbjct: 82 L-LRSHYERIVYPYE 95
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKA-ISKKIGVLWSNLTEAEKQVYQEKGLK 304
DP+ PK S + F +E+ ++K + G +KK+G +WS + +KQ Y++K K
Sbjct: 5 DPNAPKRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAK 64
Query: 305 DKERYKSEMLEYRS 318
KE+Y+ ++ YR+
Sbjct: 65 LKEKYEKDIAAYRA 78
>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 = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 41/78 (52%), Gaps = 7/78 (8%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARLKPH----YYGQEKAISKKIGVLWSNLTEAEKQVYQEK 301
DP+ PK S Y FF E+ ++ +GQ + KK+G W LT EKQ Y+ K
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQ---VGKKLGEKWKALTPEEKQPYEAK 73
Query: 302 GLKDKERYKSEMLEYRSS 319
DK+RY+SE Y ++
Sbjct: 74 AQADKKRYESEKELYNAT 91
>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 = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARL---KPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKG 302
DP+ PK S Y FF E + P AI K IG W+ L++ EK+ Y+
Sbjct: 19 DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMS 78
Query: 303 LKDKERYKSEMLEY 316
+D+ RY+ E EY
Sbjct: 79 DEDRVRYEREKAEY 92
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 41/78 (52%), Gaps = 7/78 (8%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARLKPH----YYGQEKAISKKIGVLWSNLTEAEKQVYQEK 301
DP+ PK S Y FF E+ ++ +GQ + KK+G W LT EKQ Y+ K
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQ---VGKKLGEKWKALTPEEKQPYEAK 73
Query: 302 GLKDKERYKSEMLEYRSS 319
DK+RY+SE Y ++
Sbjct: 74 AQADKKRYESEKELYNAT 91
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein
Length = 100
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 56 LEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTIT 115
+ F + G K+P V K LDL+ L V GG + +DRRW V ++P
Sbjct: 18 IAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKN 77
Query: 116 SASFVLRKYYLSLLYHFE 133
S +LR +Y ++Y +E
Sbjct: 78 IGS-LLRSHYERIIYPYE 94
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 7/78 (8%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARLKPH----YYGQEKAISKKIGVLWSNLTEAEKQVYQEK 301
DP+ P+ S Y FF + A +K +G+ +SK + +W L E +KQVY++K
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGE---VSKIVASMWDGLGEEQKQVYKKK 70
Query: 302 GLKDKERYKSEMLEYRSS 319
K+ Y ++ YR+S
Sbjct: 71 TEAAKKEYLKQLAAYRAS 88
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 249 RPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKER 308
+PK RS YN + AE + K QEK K + W NL+++EK++Y + +D+ R
Sbjct: 114 KPKRPRSAYNVYVAERFQEAKGDS-PQEKL--KTVKENWKNLSDSEKELYIQHAKEDETR 170
Query: 309 YKSEM 313
Y +EM
Sbjct: 171 YHNEM 175
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 249 RPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKER 308
+PK RS YN + AE + K QEK K + W NL+++EK++Y + +D+ R
Sbjct: 2 KPKRPRSAYNVYVAERFQEAKGDS-PQEKL--KTVKENWKNLSDSEKELYIQHAKEDETR 58
Query: 309 YKSEM 313
Y +EM
Sbjct: 59 YHNEM 63
>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 = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKA-ISKKIGVLWSNLTEAEKQVYQEKGLK 304
DP+ PK S + F +E+ ++K + G ++KK+G +W+N +KQ Y++K K
Sbjct: 3 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 62
Query: 305 DKERYKSEMLEYRS 318
KE+Y+ ++ YR+
Sbjct: 63 LKEKYEKDIAAYRA 76
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 248 SRPKSNRSGYNFFFAEHYARLKPHYYGQE-KAISKKIGVLWSNLTEAEKQVYQEKGLKDK 306
S PK+ +GY F E +++ + I+K +G WS L AEKQ Y ++ K+K
Sbjct: 6 SGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEK 65
Query: 307 ERYKSEMLEYRSS 319
++Y E+ Y+ S
Sbjct: 66 QQYLKELWAYQQS 78
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4
Demethylase Rbp2
Length = 96
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 52 FWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFP 111
F L F + G K+P V K LDL+ L V S+GG V ++++W +V +
Sbjct: 11 FLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYL 70
Query: 112 TTITSASFVLRKYYLSLLYHFE 133
+ S +L+ +Y +LY +E
Sbjct: 71 PGKGTGS-LLKSHYERILYPYE 91
>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein
Length = 122
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 64 GDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRK 123
G K+P V K LDL +L V GG V +DR+W ++ F S + R
Sbjct: 29 GSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHI-RG 87
Query: 124 YYLSLL 129
+Y +L
Sbjct: 88 HYERIL 93
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 249 RPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKER 308
+PK RS YN + AE + K QEK K + W NL+++EK++Y + +D+ R
Sbjct: 146 KPKRPRSAYNVYVAERFQEAKGDS-PQEKL--KTVKENWKNLSDSEKELYIQHAKEDETR 202
Query: 309 YKSE 312
Y +E
Sbjct: 203 YHNE 206
>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 = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 3/74 (4%)
Query: 246 DPSRPKSNRSGYNFFFA---EHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKG 302
DP +P+ S Y FF E + + P SKK W ++ EK +++
Sbjct: 4 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 303 LKDKERYKSEMLEY 316
DK RY+ EM Y
Sbjct: 64 KADKARYEREMKTY 77
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 3/74 (4%)
Query: 246 DPSRPKSNRSGYNFFFA---EHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKG 302
DP +P+ S Y FF E + + P SKK W ++ EK +++
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 71
Query: 303 LKDKERYKSEMLEY 316
DK RY+ EM Y
Sbjct: 72 KADKARYEREMKTY 85
Score = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKA-ISKKIGVLWSNLTEAEKQVYQEKGLK 304
DP+ PK S + F +E+ ++K + G ++KK+G +W+N +KQ Y++K K
Sbjct: 98 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 157
Query: 305 DKERYKSEMLEYRS 318
KE+Y+ ++ YR+
Sbjct: 158 LKEKYEKDIAAYRA 171
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 35.8 bits (81), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 3/74 (4%)
Query: 246 DPSRPKSNRSGYNFFFA---EHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKG 302
DP +P+ S Y FF E + + P SKK W ++ EK +++
Sbjct: 4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 303 LKDKERYKSEMLEY 316
DK RY+ EM Y
Sbjct: 64 KADKARYEREMKTY 77
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 246 DPSRPKSNRSGYNFFFA---EHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKG 302
DP++P+ S Y FF E + + P SKK W ++ EK +++
Sbjct: 5 DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMA 64
Query: 303 LKDKERYKSEM 313
DK RY EM
Sbjct: 65 KSDKARYDREM 75
>pdb|2RQ5|A Chain A, Solution Structure Of The At-Rich Interaction Domain
(Arid) Of JumonjiJARID2
Length = 121
Score = 35.0 bits (79), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 32/68 (47%)
Query: 68 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 127
++P +GG LDL F + GG+ +V ++W ++ + P T L++ Y
Sbjct: 33 ELPLIGGCELDLACFFRLINEMGGMQQVTDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQ 92
Query: 128 LLYHFEQV 135
L ++ +
Sbjct: 93 YLLSYDSL 100
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 246 DPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKA-ISKKIGVLWSNLTEAEKQVYQEKGLK 304
DP+ PK S + F +E+ ++K + G ++KK+G +W+N +KQ Y++K K
Sbjct: 85 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 144
Query: 305 DKERYKSEMLEYRSS 319
KE+Y+ ++ YR+
Sbjct: 145 LKEKYEKDIAAYRAK 159
>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 = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 250 PKSNRSGYNFFFAEHYARLKPHYYGQEKA-ISKKIGVLWSNLTEAEKQVYQEKGLKDKER 308
PK S + F +E+ ++K + G ++KK+G +W+N +KQ Y++K K KE+
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK 62
Query: 309 YKSEMLEYRS 318
Y+ ++ YR+
Sbjct: 63 YEKDIAAYRA 72
>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 = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 250 PKSNRSGYNFFFAEHYARLKPHYYGQEKA-ISKKIGVLWSNLTEAEKQVYQEKGLKDKER 308
PK S + F +E+ ++K + G ++KK+G +W+N +KQ Y++K K KE+
Sbjct: 5 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK 64
Query: 309 YKSEMLEYRS 318
Y+ ++ YR+
Sbjct: 65 YEKDIAAYRA 74
>pdb|4FDW|A Chain A, Crystal Structure Of A Leucine Rich Hypothetical Protein
(Bacova_01565) From Bacteroides Ovatus Atcc 8483 At 2.05
A Resolution
Length = 401
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 9/81 (11%)
Query: 138 FRREAPSSSMPDAVSGSSLDNGSASPEEGSTINQLGSQGISKLQIGCSVSGV-IDGKFDN 196
+++++PS++ P G+SL++ S I QL ++ I L ++G+ + GK+D+
Sbjct: 5 YKKDSPSAANPVEPIGASLEDFS--------IEQLPAKTIYALGENIDLTGLNVTGKYDD 56
Query: 197 GYLVTVNLGSEQLKGVLYHIP 217
G V + SEQ+ G +P
Sbjct: 57 GKQRPVKVTSEQISGFSSSVP 77
>pdb|1IG6|A Chain A, Human Mrf-2 Domain, Nmr, 11 Structures
pdb|2OEH|A Chain A, Determination Of The Three-Dimensional Structure Of The
Mrf2-Dna Complex Using Paramagnetic Spin Labeling
Length = 107
Score = 32.3 bits (72), Expect = 0.40, Method: Composition-based stats.
Identities = 18/76 (23%), Positives = 34/76 (44%)
Query: 68 KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 127
++P +G K ++L +F GG + R+WK + TSA+ R++Y
Sbjct: 24 RIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYER 83
Query: 128 LLYHFEQVYYFRREAP 143
L+ +E+ + P
Sbjct: 84 LILPYERFIKGEEDKP 99
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 32.0 bits (71), Expect = 0.50, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 279 ISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYR 317
I+KK G +W L + K +++ KDK+RY EM Y+
Sbjct: 34 IAKKGGEMWKELKDKSK--WEDAAAKDKQRYHDEMRNYK 70
>pdb|2LI6|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Yeast
Protein
Length = 116
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 48 SSDLFWATLEAFHKSFGDKFK--------VPTVGGKALDLHRLFVEVTSRGGLGKVIRDR 99
S++L E F KS + K +P +G + ++L L++ V GG +V R +
Sbjct: 12 STELNNKQYELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQ 71
Query: 100 RWKEV 104
+W V
Sbjct: 72 QWSMV 76
>pdb|1L8Y|A Chain A, Solution Structure Of Hmg Box 5 In Human Upstream Binding
Factor
pdb|1L8Z|A Chain A, Solution Structure Of Hmg Box 5 In Human Upstream Binding
Factor
pdb|2HDZ|A Chain A, Crystal Structure Analysis Of The Ubf Hmg Box5
Length = 91
Score = 31.6 bits (70), Expect = 0.70, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 28/43 (65%)
Query: 281 KKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDST 323
K + + W+N+ + EK ++ +K +D++RY+ E+ E R+ +T
Sbjct: 36 KAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAAT 78
>pdb|1KKX|A Chain A, Solution Structure Of The Dna-Binding Domain Of Adr6
pdb|1KN5|A Chain A, Solution Structure Of Arid Domain Of Adr6 From
Saccharomyces Cerevisiae
Length = 123
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 57 EAFHKSFGDKFK--------VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEV 104
E F KS + K +P +G + ++L L++ V GG +V R ++W V
Sbjct: 20 ELFMKSLIENCKKRNMPLQSIPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMV 75
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 3/71 (4%)
Query: 249 RPKSNRSGYNFFFA---EHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKD 305
+P+ S Y FF E + + P SKK W ++ EK +++ D
Sbjct: 1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60
Query: 306 KERYKSEMLEY 316
K RY+ EM Y
Sbjct: 61 KARYEREMKTY 71
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 26/65 (40%), Gaps = 3/65 (4%)
Query: 255 SGYNFFFA---EHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKS 311
S Y FF E + + P SKK W ++ EK + E DK RY
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 312 EMLEY 316
EM +Y
Sbjct: 81 EMKDY 85
>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 = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 248 SRPKSNRSGYNFFFAEHYARLK-----PHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKG 302
++P R F AR K PH + E +SK +G LW L E+EK+ + E+
Sbjct: 26 NKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAE--LSKTLGKLWRLLNESEKRPFVEEA 83
Query: 303 LKDKERYKSEMLEYR 317
+ + ++K + +Y+
Sbjct: 84 ERLRVQHKKDHPDYK 98
>pdb|4FD0|A Chain A, Crystal Structure Of A Leucine Rich Hypothetical Protein
(Baccac_03700) From Bacteroides Caccae Atcc 43185 At
2.07 A Resolution
Length = 404
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 138 FRREAPSSSMPDAVSGSSLDNGSASPEEGSTINQLGSQGISKLQIGCSVSGV-IDGKFDN 196
+++++PS+ P G+ L++ S I QL ++ I L ++G+ + GK+D+
Sbjct: 8 YKKDSPSAENPAEPVGALLEDFS--------IEQLPAKTIYALGENIDLTGLNVTGKYDD 59
Query: 197 GYLVTVNLGSEQLKG 211
G V + EQ+ G
Sbjct: 60 GKQRPVKVTPEQISG 74
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
0.315 0.131 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,076,006
Number of Sequences: 62578
Number of extensions: 351332
Number of successful extensions: 691
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 40
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 627
Number of HSP's gapped (non-prelim): 50
length of query: 326
length of database: 14,973,337
effective HSP length: 99
effective length of query: 227
effective length of database: 8,778,115
effective search space: 1992632105
effective search space used: 1992632105
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 51 (24.3 bits)