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= 046368
(388 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 = 61.2 bits (147), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 42/65 (64%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
IPI+ + LDL L+V VT +GG+ ++I ++ W+E+T N P++ T+A+F LR Y
Sbjct: 56 IPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKY 115
Query: 61 LRDYE 65
L YE
Sbjct: 116 LYPYE 120
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead
Ringer Protein
Length = 128
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 39/65 (60%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
+PI+ LDL+ L+ V ARGG+ +I ++ W+E+ + PS+ T+A+F LR Y
Sbjct: 44 LPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAAFTLRTQYMKY 103
Query: 61 LRDYE 65
L YE
Sbjct: 104 LYPYE 108
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex
Length = 139
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 38/65 (58%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
+PI+ LDL+ L+ V ARGG+ +I ++ W+E+ + PS+ T+A+ LR Y
Sbjct: 46 LPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAALTLRTQYMKY 105
Query: 61 LRDYE 65
L YE
Sbjct: 106 LYPYE 110
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 43/71 (60%), Gaps = 1/71 (1%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALKDKER 258
PK SG+ F +E ++K +PG ++++ +GE+WN L +SEK Y KA K KE+
Sbjct: 10 PKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEK 69
Query: 259 YRIEMEDYRER 269
Y ++ DY+ +
Sbjct: 70 YEKDVADYKSK 80
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALK 254
DP PK S + F +E ++K HPG + ++ +GE+W++ +K Y++KA K
Sbjct: 4 DPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAK 63
Query: 255 DKERYRIEMEDYRER 269
KE+Y ++ YR +
Sbjct: 64 LKEKYEKDIAAYRAK 78
>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid
Length = 120
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 39/60 (65%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
+P +G K LDL+RL+V V GG+ ++ K ++W+E+ N ++++ AS + ++Y Q L
Sbjct: 42 LPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQCL 101
>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE
HUMAN Jarid1c Protein
Length = 117
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
IP + + LDL+ L V GG E I K+RRW V N+P N +LR +Y+ +
Sbjct: 32 IPNVERRILDLYSLSKIVVEEGGYEAICKDRRWARVAQRLNYPP-GKNIGSLLRSHYERI 90
Query: 61 LRDYE 65
+ YE
Sbjct: 91 VYPYE 95
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 38/61 (62%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
+P +G K LDL RL+V V GG+ ++ K ++W+E+ N ++++ AS + ++Y Q L
Sbjct: 43 LPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQYL 102
Query: 61 L 61
Sbjct: 103 F 103
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALK 254
DP PK S + F +E ++K HPG + ++ +GE+W++ +K Y++KA K
Sbjct: 5 DPNAPKRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAK 64
Query: 255 DKERYRIEMEDYRER 269
KE+Y ++ YR +
Sbjct: 65 LKEKYEKDIAAYRAK 79
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALK 254
DP P+ S Y FF + A +K +P E+S+++ +W+ L E +K VY++K
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEA 73
Query: 255 DKERYRIEMEDYRERL 270
K+ Y ++ YR L
Sbjct: 74 AKKEYLKQLAAYRASL 89
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein
Length = 100
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
IP + K LDL+ L V GG E I K+RRW V ++P N +LR +Y+ +
Sbjct: 31 IPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPP-GKNIGSLLRSHYERI 89
Query: 61 LRDYE 65
+ YE
Sbjct: 90 IYPYE 94
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4
Demethylase Rbp2
Length = 96
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNF-PSTATNASFVLRKYYQS 59
IP++ K LDL+ L V ++GG E + KE++W +V + + P T + +L+ +Y+
Sbjct: 28 IPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGS--LLKSHYER 85
Query: 60 LLRDYE 65
+L YE
Sbjct: 86 ILYPYE 91
>pdb|2RQ5|A Chain A, Solution Structure Of The At-Rich Interaction Domain
(Arid) Of JumonjiJARID2
Length = 121
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
+P+IGG ELDL F + GG++++ ++W ++ + P TA + L++ Y
Sbjct: 34 LPLIGGCELDLACFFRLINEMGGMQQVTDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQY 93
Query: 61 LRDYEQI 67
L Y+ +
Sbjct: 94 LLSYDSL 100
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 43/70 (61%), Gaps = 1/70 (1%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHPGKDR-EISRMIGELWNKLKESEKAVYQEKALKDKER 258
PK +GY F E+ +++ HP EI++M+G W+KL+ +EK Y ++A K+K++
Sbjct: 8 PKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQ 67
Query: 259 YRIEMEDYRE 268
Y E+ Y++
Sbjct: 68 YLKELWAYQQ 77
>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 = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHP--GKD-REISRMIGELWNKLKESEKAVYQEKA 252
DP PK S Y FF E+ + +P KD I +MIG WN L + EK Y+ +
Sbjct: 19 DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMS 78
Query: 253 LKDKERYRIEMEDYRER 269
+D+ RY E +Y +R
Sbjct: 79 DEDRVRYEREKAEYAQR 95
>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 = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
IP++ K LDL+ L V GG+E+ K+R+W +V +PS+ + + L+ +Y+ +
Sbjct: 36 IPMVERKALDLYTLHRIVQEEGGMEQTTKDRKWAKVANRMQYPSSKSVGA-TLKAHYERI 94
Query: 61 LRDYE 65
L +E
Sbjct: 95 LHPFE 99
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 196 DPAHPKPNRSGYNFFFA---EQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKA 252
DP P+ S Y FF E+H + P E S+ E W + EK +++ A
Sbjct: 4 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 253 LKDKERYRIEMEDY 266
DK RY EM+ Y
Sbjct: 64 KADKARYEREMKTY 77
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 205 SGYNFFFA---EQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERYRI 261
S Y FF E+H + P P E S+ E W + EK+ + E A DK RY
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 262 EMEDY 266
EM+DY
Sbjct: 81 EMKDY 85
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 31/74 (41%), Gaps = 3/74 (4%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD---REISRMIGELWNKLKESEKAVYQEKA 252
DP P+ S Y FF K HP E S+ E W + EK +++ A
Sbjct: 4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 253 LKDKERYRIEMEDY 266
DK RY EM+ Y
Sbjct: 64 KADKARYEREMKTY 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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
IP +G K+++L +F GG E I R+WK + +T+A+ R++Y+ L
Sbjct: 25 IPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERL 84
Query: 61 LRDYEQ 66
+ YE+
Sbjct: 85 ILPYER 90
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHPG-KDREISRMIGELWNKLKESEKAVYQEKALKDKER 258
PK + + + + +K +PG K EI++ GE+W +LK+ K+ +++ A KDK+R
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKD--KSKWEDAAAKDKQR 61
Query: 259 YRIEMEDYR 267
Y EM +Y+
Sbjct: 62 YHDEMRNYK 70
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 31/74 (41%), Gaps = 3/74 (4%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD---REISRMIGELWNKLKESEKAVYQEKA 252
DP P+ S Y FF K HP E S+ E W + EK +++ A
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 71
Query: 253 LKDKERYRIEMEDY 266
DK RY EM+ Y
Sbjct: 72 KADKARYEREMKTY 85
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALK 254
DP PK S + F +E ++K HPG ++++ +GE+WN +K Y++KA K
Sbjct: 98 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 157
Query: 255 DKERYRIEMEDYRER 269
KE+Y ++ YR +
Sbjct: 158 LKEKYEKDIAAYRAK 172
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKDR-EISRMIGELWNKLKESEKAVYQEKALK 254
DP PK S Y FF E ++ +P ++ + +GE W L EK Y+ KA
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQA 76
Query: 255 DKERYRIEMEDYRERL 270
DK+RY E E Y L
Sbjct: 77 DKKRYESEKELYNATL 92
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKDR-EISRMIGELWNKLKESEKAVYQEKALK 254
DP PK S Y FF E ++ +P ++ + +GE W L EK Y+ KA
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQA 76
Query: 255 DKERYRIEMEDYRERL 270
DK+RY E E Y L
Sbjct: 77 DKKRYESEKELYNATL 92
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD---REISRMIGELWNKLKESEKAVYQEKA 252
DP P+ S Y FF K HP E S+ E W + EK+ +++ A
Sbjct: 5 DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMA 64
Query: 253 LKDKERYRIEMED 265
DK RY EM++
Sbjct: 65 KSDKARYDREMKN 77
>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 = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERY 259
PK RS YN + AE+ K P +E + + E W L +SEK +Y + A +D+ RY
Sbjct: 115 PKRPRSAYNVYVAERFQEAKGDSP---QEKLKTVKENWKNLSDSEKELYIQHAKEDETRY 171
Query: 260 RIEMEDYRERL 270
EM+ + E++
Sbjct: 172 HNEMKSWEEQM 182
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHP-GKDREISRMIGELWNKLKESEKAVYQEKALKDKER 258
PK S Y F EQ K +P K E+ R I + W +L +S+K +YQ+ + +
Sbjct: 10 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQV 69
Query: 259 YRIEMEDYRERLKTGQVIS 277
Y+ E+ ++E+L Q++S
Sbjct: 70 YKEEISRFKEQLTPSQIMS 88
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERY 259
PK RS YN + AE+ K P +E + + E W L +SEK +Y + A +D+ RY
Sbjct: 3 PKRPRSAYNVYVAERFQEAKGDSP---QEKLKTVKENWKNLSDSEKELYIQHAKEDETRY 59
Query: 260 RIEMEDY 266
EM+ +
Sbjct: 60 HNEMKSW 66
>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 = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALK 254
DP PK S + F +E ++K HPG ++++ +GE+WN +K Y++KA K
Sbjct: 3 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 62
Query: 255 DKERYRIEMEDYRER 269
KE+Y ++ YR +
Sbjct: 63 LKEKYEKDIAAYRAK 77
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 200 PKPNRSGYNFFFA---EQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDK 256
P+ S Y FF E+H + P E S+ E W + EK +++ A DK
Sbjct: 2 PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK 61
Query: 257 ERYRIEMEDY 266
RY EM+ Y
Sbjct: 62 ARYEREMKTY 71
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERY 259
PK RS YN + AE+ K P +E + + E W L +SEK +Y + A +D+ RY
Sbjct: 147 PKRPRSAYNVYVAERFQEAKGDSP---QEKLKTVKENWKNLSDSEKELYIQHAKEDETRY 203
Query: 260 RIEMEDYRE 268
E + + E
Sbjct: 204 HNEXKSWEE 212
Score = 35.4 bits (80), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHP-GKDREISRMIGELWNKLKESEKAVYQEKALKDKER 258
PK S Y F EQ K +P K E+ R I + W +L +S+K +YQ+ + +
Sbjct: 42 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQV 101
Query: 259 YRIEMEDYRERLKTGQVIS 277
Y+ E+ ++E+L Q+ S
Sbjct: 102 YKEEISRFKEQLTPSQIXS 120
>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein
Length = 122
Score = 34.7 bits (78), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNF-PSTATNASFVLRKYYQS 59
IP + K LDL +L V GG + K+R+W ++ F P A + +R +Y+
Sbjct: 34 IPHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSH--IRGHYER 91
Query: 60 LLRDYEQIYFFRSQDS 75
+L Y F S DS
Sbjct: 92 ILNPYN---LFLSGDS 104
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 197 PAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVY--QEKAL 253
P K + + F + ++PGKD R IS ++G+ W K+K E+ +Y + KAL
Sbjct: 15 PNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKAL 74
Query: 254 KDKER 258
++++
Sbjct: 75 AEEQK 79
>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 = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALKDKER 258
PK S + F +E ++K HPG ++++ +GE+WN +K Y++KA K KE+
Sbjct: 5 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK 64
Query: 259 YRIEMEDYRERLK 271
Y ++ YR + K
Sbjct: 65 YEKDIAAYRAKGK 77
>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 = 0.15, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 200 PKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALKDKER 258
PK S + F +E ++K HPG ++++ +GE+WN +K Y++KA K KE+
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK 62
Query: 259 YRIEMEDYRERLK 271
Y ++ YR + K
Sbjct: 63 YEKDIAAYRAKGK 75
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 197 PAHPKPNRSGYNFFFAEQHARLKPLHPG-KDREISRMIGELWNKLKESEKAVYQEKALKD 255
P PK + Y FF E+ A+ LHP + ++++++ + + +L E +K Y + ++
Sbjct: 8 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQRE 67
Query: 256 KERYRIEMEDYRE 268
K+ + + +RE
Sbjct: 68 KQEFERNLARFRE 80
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 196 DPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALK 254
DP PK S + F +E ++K HPG ++++ +GE+WN +K Y++KA K
Sbjct: 85 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 144
Query: 255 DKERYRIEMEDYRER 269
KE+Y ++ YR +
Sbjct: 145 LKEKYEKDIAAYRAK 159
>pdb|3MGX|A Chain A, Crystal Structure Of P450 Oxyd That Is Involved In The
Biosynthesis Of Vancomycin-Type Antibiotics
pdb|3MGX|B Chain B, Crystal Structure Of P450 Oxyd That Is Involved In The
Biosynthesis Of Vancomycin-Type Antibiotics
Length = 415
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 18/91 (19%)
Query: 201 KPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERYR 260
P+ SG +H + R++ +++G L ++ A K ER R
Sbjct: 97 HPDNSGGRMMVVSEHE--------QHRKLRKLVGPLLSR----------AAARKLAERVR 138
Query: 261 IEMEDYRERLKTGQVISDAIPLQQRLPGADV 291
IE+ D R+ G+V A + R+P A V
Sbjct: 139 IEVGDVLGRVLDGEVCDAATAIGPRIPAAVV 169
>pdb|2YRW|A Chain A, Crystal Structure Of Gar Synthetase From Geobacillus
Kaustophilus
pdb|2YRX|A Chain A, Crystal Structure Of Gar Synthetase From Geobacillus
Kaustophilus
pdb|2YS6|A Chain A, Crystal Structure Of Gar Synthetase From Geobacillus
Kaustophilus
pdb|2YS7|A Chain A, Crystal Structure Of Gar Synthetase From Geobacillus
Kaustophilus
Length = 451
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 71 RSQDSWQGPSTNAVSAPGTAQPSPDIQSAVQQPRINAAVLPEARPASSGGSPVIGVI 127
R+ D +GP+T + G P P I + + A + P A+ ++ G P +GV+
Sbjct: 236 RAYDGDEGPNTGGM---GAYSPVPQISDEMMDAALEAILRPAAKALAAEGRPFLGVL 289
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 29.3 bits (64), Expect = 4.1, Method: Composition-based stats.
Identities = 13/42 (30%), Positives = 27/42 (64%)
Query: 228 EISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRER 269
EIS+ +G+ W LK+S+K + ++A + + ++ + DY+ R
Sbjct: 32 EISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYR 73
>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 = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 27/40 (67%)
Query: 228 EISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYR 267
E+S+ +G+LW L ESEK + E+A + + +++ + DY+
Sbjct: 59 ELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYK 98
>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 = 28.1 bits (61), Expect = 9.0, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEV 36
IP IG ++++L L++ V GG +++ + ++W V
Sbjct: 40 IPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMV 75
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
0.311 0.131 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,966,396
Number of Sequences: 62578
Number of extensions: 503709
Number of successful extensions: 894
Number of sequences better than 100.0: 58
Number of HSP's better than 100.0 without gapping: 46
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 827
Number of HSP's gapped (non-prelim): 63
length of query: 388
length of database: 14,973,337
effective HSP length: 101
effective length of query: 287
effective length of database: 8,652,959
effective search space: 2483399233
effective search space used: 2483399233
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: 52 (24.6 bits)