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= 020330
(327 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 = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 37 FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
F D L F GT IP++ + LDL +LYV T +GG +V+ +K WRE+
Sbjct: 38 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNL 97
Query: 96 SPTTTSASFVLRKHYLTLLYHYE 118
+ TSA+F LR Y+ LY YE
Sbjct: 98 PTSITSAAFTLRTQYMKYLYPYE 120
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4
Demethylase Rbp2
Length = 96
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 32/82 (39%), Positives = 47/82 (57%), Gaps = 1/82 (1%)
Query: 37 FWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFS 96
F D L +F + G+ IPV+ K LDL+ L ++GG+E V EKKW +VG+ +
Sbjct: 11 FLDQLAKFWELQGSTLKIPVVERKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYL 70
Query: 97 PTTTSASFVLRKHYLTLLYHYE 118
P + S +L+ HY +LY YE
Sbjct: 71 PGKGTGS-LLKSHYERILYPYE 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 = 55.1 bits (131), Expect = 5e-08, Method: Composition-based stats.
Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNREREFT---KMIGESWTNLSPEERKVYQNIG 299
DP+ PK S Y FF EK ++ + P ++ KMIG +W LS EE+K Y+ +
Sbjct: 19 DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMS 78
Query: 300 LKDKERYNRELKEYKER 316
+D+ RY RE EY +R
Sbjct: 79 DEDRVRYEREKAEYAQR 95
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead
Ringer Protein
Length = 128
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 37 FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
F D L F GT +P++ LDL+ LY RGG V+ +K W+E+
Sbjct: 26 FLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHL 85
Query: 96 SPTTTSASFVLRKHYLTLLYHYE 118
+ TSA+F LR Y+ LY YE
Sbjct: 86 PSSITSAAFTLRTQYMKYLYPYE 108
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex
Length = 139
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 37 FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
F D L F GT +P++ LDL+ LY RGG V+ +K W+E+
Sbjct: 28 FLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHL 87
Query: 96 SPTTTSASFVLRKHYLTLLYHYE 118
+ TSA+ LR Y+ LY YE
Sbjct: 88 PSSITSAALTLRTQYMKYLYPYE 110
>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN
Jarid1c Protein
Length = 117
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 1/95 (1%)
Query: 24 LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
++ E ++ + + D + +F I G+ IP + + LDL+ L GGYE + +
Sbjct: 2 MNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKD 61
Query: 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
++W V + P S LR HY ++Y YE
Sbjct: 62 RRWARVAQRLNYPPGKNIGSL-LRSHYERIVYPYE 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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 50/95 (52%), Gaps = 1/95 (1%)
Query: 24 LSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAE 83
L+ E ++ + F D + +F + G+ IP++ K LDL+ L+ GG E+ +
Sbjct: 6 LNELEAKTRVKLNFLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKD 65
Query: 84 KKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
+KW +V ++ P++ S L+ HY +L+ +E
Sbjct: 66 RKWAKVANRMQY-PSSKSVGATLKAHYERILHPFE 99
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein
Length = 100
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 1/94 (1%)
Query: 25 SSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEK 84
SS ++ + + D + +F I G+ IP + K LDL+ L GGYE + ++
Sbjct: 2 SSGSSGTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDR 61
Query: 85 KWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYE 118
+W V + P S +LR HY ++Y YE
Sbjct: 62 RWARVAQRLHYPPGKNIGS-LLRSHYERIIYPYE 94
>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 = 48.1 bits (113), Expect = 7e-06, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 39/66 (59%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
IP +G K+++L ++ A GGYE + A ++W+ + +P +TSA+ R+HY L
Sbjct: 25 IPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERL 84
Query: 114 LYHYEQ 119
+ YE+
Sbjct: 85 ILPYER 90
>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid
Length = 120
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
+P +G K LDL+ LYV GG +V KKWRE+ T++SA+ L+K Y+
Sbjct: 42 LPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVG-TSSSAASSLKKQYIQC 100
Query: 114 LYHYE 118
LY +E
Sbjct: 101 LYAFE 105
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE---REFTKMIGESWTNLSPEERKVYQNIG 299
DP P+ S Y FF + K +P+ EF+K E W +S +E+ ++++
Sbjct: 4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 300 LKDKERYNRELKEY 313
DK RY RE+K Y
Sbjct: 64 KADKARYEREMKTY 77
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE---REFTKMIGESWTNLSPEERKVYQNIG 299
DP+ P+ S Y FF + K +P+ EF+K E W +S +E+ ++++
Sbjct: 5 DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMA 64
Query: 300 LKDKERYNRELK 311
DK RY+RE+K
Sbjct: 65 KSDKARYDREMK 76
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 245 SYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLKDK 303
S PK +GY F E+ ++++ +P+ E TKM+G W+ L P E++ Y + K+K
Sbjct: 6 SGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEK 65
Query: 304 ERYNRELKEYKE 315
++Y +EL Y++
Sbjct: 66 QQYLKELWAYQQ 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 = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERY 306
PK RS YN + AE+ + K P E K + E+W NLS E+++Y +D+ RY
Sbjct: 115 PKRPRSAYNVYVAERFQEAKGDSPQ---EKLKTVKENWKNLSDSEKELYIQHAKEDETRY 171
Query: 307 NRELKEYKERL 317
+ E+K ++E++
Sbjct: 172 HNEMKSWEEQM 182
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 245 SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDK 303
S PK S Y F E+ K+ P+ + E + I + W L ++K+YQ+ +
Sbjct: 8 SCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEW 67
Query: 304 ERYNRELKEYKERL 317
+ Y E+ +KE+L
Sbjct: 68 QVYKEEISRFKEQL 81
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE---REFTKMIGESWTNLSPEERKVYQNIG 299
DP P+ S Y FF + K +P+ EF+K E W +S +E+ ++++
Sbjct: 4 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 300 LKDKERYNRELKEY 313
DK RY RE+K Y
Sbjct: 64 KADKARYEREMKTY 77
>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 = 44.3 bits (103), Expect = 9e-05, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLK 301
DP+ PK S Y FF E ++S P+ + K +GE W L+PEE++ Y+
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQA 76
Query: 302 DKERYNRELKEYKERL 317
DK+RY E + Y L
Sbjct: 77 DKKRYESEKELYNATL 92
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLK 301
DP+ PK S Y FF E ++S P+ + K +GE W L+PEE++ Y+
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQA 76
Query: 302 DKERYNRELKEYKERL 317
DK+RY E + Y L
Sbjct: 77 DKKRYESEKELYNATL 92
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE---REFTKMIGESWTNLSPEERKVYQNIG 299
DP P+ S Y FF + K +P+ EF+K E W +S +E+ ++++
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 71
Query: 300 LKDKERYNRELKEY 313
DK RY RE+K Y
Sbjct: 72 KADKARYEREMKTY 85
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLK 301
DP+ PK S + F +E K+K +P + K +GE W N + ++++ Y+ K
Sbjct: 98 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 157
Query: 302 DKERYNRELKEYKER 316
KE+Y +++ Y+ +
Sbjct: 158 LKEKYEKDIAAYRAK 172
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERY 306
PK RS YN + AE+ + K P E K + E+W NLS E+++Y +D+ RY
Sbjct: 147 PKRPRSAYNVYVAERFQEAKGDSPQ---EKLKTVKENWKNLSDSEKELYIQHAKEDETRY 203
Query: 307 NRELKEYKER 316
+ E K ++E+
Sbjct: 204 HNEXKSWEEQ 213
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 245 SYPKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDK 303
S PK S Y F E+ K+ P+ + E + I + W L ++K+YQ+ +
Sbjct: 40 SCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEW 99
Query: 304 ERYNRELKEYKERL 317
+ Y E+ +KE+L
Sbjct: 100 QVYKEEISRFKEQL 113
>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein
Length = 122
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 1/93 (1%)
Query: 25 SSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEK 84
SS E ++ + F D + ++ + G+ IP + K LDL L GG+ V ++
Sbjct: 5 SSGEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKILDLFQLNKLVAEEGGFAVVCKDR 64
Query: 85 KWREVGAVFKFSPTTTSASFVLRKHYLTLLYHY 117
KW ++ F+P S + R HY +L Y
Sbjct: 65 KWTKIATKMGFAPGKAVGSHI-RGHYERILNPY 96
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
+P +G K LDL LYV GG +V KKWRE+ T++SA+ L+K Y+
Sbjct: 43 LPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVG-TSSSAASSLKKQYIQY 101
Query: 114 LYHYE 118
L+ +E
Sbjct: 102 LFAFE 106
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERY 306
PK RS YN + AE+ + K P +E K + E+W NLS E+++Y +D+ RY
Sbjct: 3 PKRPRSAYNVYVAERFQEAKGDSP---QEKLKTVKENWKNLSDSEKELYIQHAKEDETRY 59
Query: 307 NRELKEY 313
+ E+K +
Sbjct: 60 HNEMKSW 66
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 252 SGYNFFFA---EKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNR 308
S Y FF E+H K P EF+K E W +S +E+ + + DK RY+R
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 309 ELKEY 313
E+K+Y
Sbjct: 81 EMKDY 85
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNRE---REFTKMIGESWTNLSPEERKVYQNIGLKDK 303
P+ S Y FF + K +P+ EF+K E W +S +E+ ++++ DK
Sbjct: 2 PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK 61
Query: 304 ERYNRELKEY 313
RY RE+K Y
Sbjct: 62 ARYEREMKTY 71
>pdb|2RQ5|A Chain A, Solution Structure Of The At-Rich Interaction Domain
(Arid) Of JumonjiJARID2
Length = 121
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
+P+IGG ELDL + GG ++V KKW ++ + + T L++ Y
Sbjct: 34 LPLIGGCELDLACFFRLINEMGGMQQVTDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQY 93
Query: 114 LYHYEQV 120
L Y+ +
Sbjct: 94 LLSYDSL 100
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLKDKER 305
PK SG+ F +E K+KS P + K +GE W NL+ E++ Y K KE+
Sbjct: 10 PKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEK 69
Query: 306 YNRELKEYKER 316
Y +++ +YK +
Sbjct: 70 YEKDVADYKSK 80
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLK 301
DP+ P+ S Y FF + +K PN E +K++ W L E+++VY+
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEA 73
Query: 302 DKERYNRELKEYKERL 317
K+ Y ++L Y+ L
Sbjct: 74 AKKEYLKQLAAYRASL 89
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLK 301
DP+ PK S + F +E K+KS +P + K +GE W+ S ++++ Y+ K
Sbjct: 4 DPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAK 63
Query: 302 DKERYNRELKEYKER 316
KE+Y +++ Y+ +
Sbjct: 64 LKEKYEKDIAAYRAK 78
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLK 301
DP+ PK S + F +E K+KS +P + K +GE W+ S ++++ Y+ K
Sbjct: 5 DPNAPKRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAK 64
Query: 302 DKERYNRELKEYKER 316
KE+Y +++ Y+ +
Sbjct: 65 LKEKYEKDIAAYRAK 79
>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 = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLK 301
DP+ PK S + F +E K+K +P + K +GE W N + ++++ Y+ K
Sbjct: 3 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 62
Query: 302 DKERYNRELKEYKER 316
KE+Y +++ Y+ +
Sbjct: 63 LKEKYEKDIAAYRAK 77
>pdb|2LI6|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Yeast
Protein
Length = 116
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
IP IG ++++L LY+ GG ++V ++W V + S S Y +
Sbjct: 41 IPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESI-----YFRI 95
Query: 114 LYHYEQVHFFKMQG 127
L YE+ H +G
Sbjct: 96 LLPYER-HMISQEG 108
>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 = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 54 IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTL 113
IP IG ++++L LY+ GG ++V ++W V + S S Y +
Sbjct: 40 IPEIGNRKINLFYLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESI-----YFRI 94
Query: 114 LYHYEQVHFFKMQG 127
L YE+ H +G
Sbjct: 95 LLPYER-HMISQEG 107
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 31.2 bits (69), Expect = 0.80, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPN-REREFTKMIGESWTNLSPEERKVYQNIGLKDKER 305
PK + + + + +K P + E K GE W L +++ +++ KDK+R
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQR 61
Query: 306 YNRELKEYK 314
Y+ E++ YK
Sbjct: 62 YHDEMRNYK 70
>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 = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLKDKER 305
PK S + F +E K+K +P + K +GE W N + ++++ Y+ K KE+
Sbjct: 5 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK 64
Query: 306 YNRELKEYKERLK 318
Y +++ Y+ + 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 = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 247 PKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLKDKER 305
PK S + F +E K+K +P + K +GE W N + ++++ Y+ K KE+
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK 62
Query: 306 YNRELKEYKERLK 318
Y +++ Y+ + K
Sbjct: 63 YEKDIAAYRAKGK 75
>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 = 28.9 bits (63), Expect = 3.8, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 25/46 (54%)
Query: 269 YPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYK 314
+ N + K + +W N+ +E+ ++ +D++RY REL E +
Sbjct: 27 FKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMR 72
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 244 PSYPKPNRSGYNFFFAEKHYKLKSLYPNRER-EFTKMIGESWTNLSPEERKV-YQNIGLK 301
P +PK + Y FF EK K L+P + TK++ + + L PE++K+ Y +
Sbjct: 8 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKEL-PEKKKMKYIQDFQR 66
Query: 302 DKERYNRELKEYKE 315
+K+ + R L ++E
Sbjct: 67 EKQEFERNLARFRE 80
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNRE-REFTKMIGESWTNLSPEERKVYQNIGLK 301
DP+ PK S + F +E K+K +P + K +GE W N + ++++ Y+ K
Sbjct: 85 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 144
Query: 302 DKERYNRELKEYKER 316
KE+Y +++ Y+ +
Sbjct: 145 LKEKYEKDIAAYRAK 159
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 28.1 bits (61), Expect = 6.7, Method: Composition-based stats.
Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 256 FFFAEKHYKLK--SLYPNRE-REFTKMIGESWTNLSPEERKVY 295
F K Y+++ +YP ++ R + ++G+ W + EER++Y
Sbjct: 25 FMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMY 67
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
0.318 0.135 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,262,406
Number of Sequences: 62578
Number of extensions: 423422
Number of successful extensions: 788
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 730
Number of HSP's gapped (non-prelim): 46
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)